In my previous post I commented on a recent paper by Jeremy Smith and colleagues (L. Hong et al., Phys. Rev. Lett. 108, 238102; 2012) in which it was shown that the coupling between the dynamics of a protein and its hydration shell can propagate from the surface to the core to soften up the entire molecule. Martin Weik at Grenoble, Frans Mulder at Aarhus and their coworkers have now investigated this idea experimentally via neutron scattering from the small protein calbindin D9k P43G deuterated in the one case on the “outside” and in the other case on the “inside” (K. Wood et al., Angew. Chem. Int. Ed. 10.1002/anie.201205898 – paper here). They find that both the exterior and the core of the protein are sensitive to hydration: the dynamics of both regions undergo a hydration-dependent dynamical transition in the same temperature range of around 250 K. In other words, this transition does appear to be a “global” one.
Ruhong Zhou at IBM Yorktown Heights is continuing to investigate how denaturants affect protein conformation and folding. In a paper with Eugene Shaknovich and coworkers, he reports the surprising finding that in a mixture of the denaturants urea and guanidinium chloride, hen egg-white lysozyme and protein L will both collapse, albeit with an increase in non-native hydrophobic contacts (Z. Xia et al., JACS 134, 18266; 2012 – paper here). The collapse (it is evidently not ‘folding’ in the proper sense) is induced by the specific interactions of the denaturants with the protein surface: GdmCl is absorbed there due to electrostatic interactions, while urea also accumulates near the first hydration shell and introduces crowding. This is a reminder of how specific, rather than generic, interactions of proteins with denaturants and osmolytes will dominate the behaviour, sometimes in non-intuitive ways.
Another counter-intuitive result is reported by Haiping Fang of the Shanghai Institute of Applied Physics and coworkers, relating to the evaporation of water molecules from solid surfaces. They find that the evaporation rate doesn’t change monotonically as one progresses from hydrophilic to hydrophobic surfaces, as one might expect, but has a maximum (S. Wang et al., J. Phys. Chem. B 116, 13863; 2012 – paper here). This follows from the fact that, while interactions between water and the surface dominate in situations where the surface is well wetted, for highly hydrophobic surfaces the water gathers into isolated ‘surface droplets’, in which case water evaporation is controlled by water-water interactions. The maximum results from a crossover between these two competing mechanisms. The findings might be important not only for, e.g. water retention in soils but also for the possibility of drying transitions in hydrophobic aggregation.
It’s become clear that even in relatively dilute solution some soluble small organic molecules may not be homogeneously dispersed. That notion is backed up by neutron-scattering experiments of Lorna Dougan at the University of Leeds and colleagues, in which they investigate glutamine solutions (N. H. Rhys et al., J. Phys. Chem. B 116, 13308; 2012 – paper here). Polyglutamine stretches of proteins are quite common and apparently important – they feature, for example, in some proteins that aggregate to induce neurodegeneration. Such aggregates seem to have collapsed polyglutamine regions, even though glutamate might be expected to form favourable hydrogen-bonding interactions with water. This motivated the present study, to investigate the interactions of glutamine monomers in water. It appears that glutamine forms some dimers via hydrogen bonds in both the ‘backbone’ and ‘side chain’ of the molecules, even at concentrations of 30 mg per mL, revealing a strong propensity to self-associate. Later work will address glutamine oligomers and polymers.
Lorna, in collaboration again with Alan Soper, has also used neutron scattering to investigate the clustering/microsegregation of the cryoprotectant glycerol in water (J. J. Towey et al., J. Phys. Chem. B 116, 13898; 2012 – paper here). They find that glycerol’s cryobiological effects don’t seem to stem from any effect it has on the hydrogen-bonding ability of water. Rather, glycerol molecules simply replace water molecules to allow the waters to retain their hydrogen-bonding capacity over a wide range of glycerol concentration. However, the presence of glycerol does segregate water into clusters at higher concentrations. So the researchers propose that the cryoprotectant activity stems not from any disruption of ‘water structure’ per se, but from glycerol’s very ability to substitute for water, while suppressing ice formation because of water segregation.
It is sobering to see that the dissociation of an ion pair such as NaCl –that’s to say, how and why salt dissolves – is still not fully understood. Andrew Ballard at the University of Maryland and Christoph Dellago of the University of Vienna present simulations of this process, using TIP4P water (J. Phys. Chem. B 116, 13490; 2012 – paper here). They say that the ion dissociation is favoured energetically but opposed entropically because of the water molecules entering the hydration shells of the ions. As in Dellago’s earlier work with Philip Geissler and David Chandler (J. Phys. Chem. B 103, 3706 (1999)), they find that the inter-ion separation is not a good reaction coordinate, as structures with different relaxation behaviour can occur for the same separation. The solvent fluctuations continue to play a role in the process over relatively long ranges, even into the third hydration shell.
It would be nice to know how that finding of a relatively long-ranged perturbation of water sits with the apparently surprising results of Sheeba Jem Irudayam of the UNC at Chapel Hill and Richard Henchman at Manchester. Their MD simulations of the hydration of alkali metal and halide ions show that this perturbation extends over remarkably long distances (J. Chem. Phys. 137, 034508; 2012 – paper here). They find non-bulk-like structural characteristics over virtually the whole simulation box (about 2.2 nm on a side for most ions, 3.3 nm for lithium and fluoride, corresponding to around 375 and 1200 TIP4P water molecules respectively). Specifically, there is a very slight but detectable excess of H-bond acceptors around halide ions, and of donors around alkali metal ions, which compensates for the shorter-ranged perturbations to water structure in the first and second hydration spheres. They also find long-ranged deviations for noble gas solutes: slightly enhanced tetrahedrality and an oscillating excess and deficiency of donors and acceptors. Similar perturbations are found for the air-water interface. The authors say that such small effects are likely to be invisible to standard spectroscopic techniques, although there have been some hints of them in neutron-scattering studies by Alan Soper and coworkers. To what extent they might have important thermodynamic consequences remain to be seen, but these results are highly intriguing.
In concentrated salt solution, ion-dependent effects on the O-D stretch are seen for both the anion and cation in pump-probe IR spectroscopic experiments by Michaal Fayer and colleagues at Stanford (C. H. Giammanco et al., J. Phys. Chem. B 116, 13781; 2012 – paper here). They find that in concentrated solutions it no longer suffices to divide water’s relaxational modes into ion-associated and water-associated fractions, because there is no longer any bulk-like component of the solvent. In this situation, water reorientational motions are highly cooperative.
Ionic hydration in confined spaces is important for a number of reasons not connected to water in biology, not least for understanding the interfacial behaviour in supercapacitors and batteries with nanoporous carbon electrodes. Tomonori Ohba of Chiba University in Japan and colleagues have explored this issue using synchrotron XRD of electrolytes inside carbon nanotubes (JACS 134, 17850; 2012 – paper here). They conclude that hydration is significantly different inside nanotubes with an average internal pore diameter of 2 nm, relative to the bulk. They can’t evaluate hydration numbers or detailed hydration structures, but say that the hydration structuring is stronger under confinement and that the hydrogen-bonded network of the solvent is correspondingly stretched and weakened. I must confess that I struggle to find an intuitive picture of what is happening here – but this perturbation is at least consistent with experiments showing a pore-size dependence of capacitance in double-layer capacitors (e.g. Chmiola et al., Science 313, 1760; 2006).
Transport of water through nanopores such as carbon nanotubes and aquaporin has important implications both for biology (e.g. functioning of ion channels) and technology (water purification). Kuiwen Zhao and Huiying Wu of Shanghai Jiao Tong University have used MD simulations to study water and ion transport through arrays of carbon nanotubes, driven by osmotic pressure (J. Phys. Chem. B 116, 13459; 2012 – paper here). In particular, they have looked at the effect of the packing density of the pores, and find that at high packing densities there can be steric interference of ions (and their hydration spheres) entering the pore mouths. There may therefore be an optimal packing density for efficient transport through the pore array, rather than simply trying to pack pores as densely as possible.
Acid or base? Yes, it’s the air-water interface again, and this time Agustín Colussi at Caltech and colleagues report experiments which seem to indicate that the interface is Brønsted basic (H. Mishra et al., PNAS 109, 18679; 2012 – paper here). They say that the controversies and discrepancies that have previously plagues this question stem at least partly from a failure to recognize acidity as a relative concept referring not so much to proton or hydroxide concentrations as to the extent of proton sharing between conjugate acid/base pairs. The researchers use electrospray ionization mass spectrometry of interfacial layers to measure the degree of dissociation of carboxylic acids both in the dissolved aqueous phase and when it collides in the gas phase with a water jet – probing, respectively, the ‘inner’ and ‘outer’ side of the surface. The detection of carboxylate ions indicates the presence of hydroxide at the surface, for all pH>2. Moreover, this surface excess of hydroxide can account for the observed negative charge at the air-water surface.
Mischa Bonn and coworkers at Mainz say that the bond orientational behaviour of water at the air-water interface is sensitive to nuclear quantum effects (Y. Nagata et al., Phys. Rev. Lett. 109, 226101; 2012 – paper here). They report quantum MD simulations showing that, while H2O and D2O have indistinguishable structures at the interface, HDO is quite distinct, with OD bonds oriented into the liquid and OH bonds oriented towards the gas phase. This would be because OD groups are able to form relatively stronger hydrogen bonds owing to a quantum isotope effect. They say this finding is in good quantitative agreement with SFG spectroscopic studies, e.g. by Geri Richmond.
The use of fluorescence microscopy to study freeze-dried biological samples can reveal details of water and ionic content of cells at the sub-cellular, nanoscale level, according to a paper by Jean Michel at the Université de Reims Champagne Ardenne in France and coworkers (F. Nolin et al., J. Struct. Biol. 180, 352; 2012 – paper here). Elemental (e.g. ion) distributions can be deduced from EDXS analysis, while specific protein densities can be studied by GFP-labelling. It looks like a nice method for deducing larger-scale patterns of hydration and ion distribution, for example that occasioned by chromatin compaction.
Water can undergo capillary evaporation from between two hydrophobic surfaces at small separations, but exactly how this happens hasn’t been fully elucidated. Sumit Sharma and Pablo Debenedetti at Princeton have investigated the process using MC simulations, and find that the outcome depends on the size of the surfaces (J. Phys. Chem. B 116, 13282; 2012 – paper here). If they are sufficiently large (3 nm square), evaporation involves the formation of a tubular cavity spanning the gap of the slit-like pore – an activated event as described by classical nucleation theory. But for 1 nm square surfaces there is too little space to accommodate such a vapour cavity, and the gap simply empties entirely.
It’s well documented that water in such confined spaces may also show reduced diffusional mobility. Hiroki Matsubara at Tohoku University in Japan and colleagues have attempted to figure out why this happens for liquids in general using MD simulations (Phys. Rev. Lett. 109, 197801; 2012 – paper here). They find that OMCTS (an alkylsiloxane) between two mica surfaces has a diffusion coefficient that depends on the surface separation, at least in the range 23-64 Å (3-7 molecular layers). This is because diffusion is an activated process, and the activation energy increases both because of the entropic constraint on some molecular configurations under confinement and the lowering of the average molecular potential energy in the gap. To what extent these effects operate and are modified for water remains to be seen.
How water mediates the association of a protein with its ligand is one of the most interesting issues concerning water’s role in molecular biology. Francesco Paesani of the University of California at San Diego and his colleagues present MD simulations which further support the notion that the water is involved as an active participant (R. Baron et al., J. Phys. Chem. B 116, 13774; 2012 – paper here). They are interested in extracting signatures of time-dependent changes in water structure and dynamics accessible to ultrafast vibrational spectroscopy. They model the binding between an apolar cavity and a spherical hydrophobic ligand, and find that the expulsion of disordered water from the cavity and suppression of slow water density fluctuations on binding result in an unfavourable entropic contribution to the binding free energy. Meanwhile, the reorientational dynamics of the water hydrating the ligand speed up as it approaches the cavity, and this water becomes less tetrahedral. This should be accompanied by the appearance of a shoulder on the O-D stretch mode for mixtures of HOD/H2O, as used in some recent spectroscopic studies, owing to the increasing concentration of dangling O-D bonds.
Francesco and his coworkers also present a new ab initio model for water, called HBB2-pol (V. Babin et al., J. Phys. Chem. Lett. 3, 3765; 2012 - paper here). They say it provides agreement with experiment from water dimers to the liquid state, capturing both the observed structural and dynamic properties while a avoiding the computational complexity that has previously rendered models such as WHBB intractable beyond small clusters.
Hydrophobicity may be the driving force behind the formation of some knots in protein structures. This idea is supported by work by Jeremy Sanders at Cambridge and colleagues, who show that a synthetic molecule composed of hydrophobic polyaromatics linked by hydrophilic amino acids will trimerize into a trefoil knot as the most effective way to ‘bury’ the hydrophobic surfaces (N. Ponnuswamy et al., Science 338, 783; 2012 – paper here).
Thursday, December 6, 2012
Thursday, November 22, 2012
Softening up proteins
It’s commonly thought that hydration of hydrophobic solutes happens with the positioning of water-water hydrogen bonds tangential to the solute surface. That notion seems to be confirmed in a neutron-scattering study by Jeremy Smith at Oak Ridge and colleagues (I. Daidone et al., Biophys. J. 103, 1518-1524; 2012 – paper here). They show that this information can be extracted from the low-Q spectra of dipeptides in water, in conjunction with MD simulations. Moreover, the degree of connectivity of the hydration water clusters is greater than that in the bulk, and increases with increasing solute hydrophobicity.
In a second paper Jeremy, with Alexei Sokolov and coworkers, use neutron scattering to look at the dynamics of (fully deuterated) GFP and its hydration shell (J. D. Nickels et al., Biophys. J. 103, 1566-1575; 2012 – paper here). The interaction between solvent and solute dynamics is complex. At lower temperatures (below about 200 K) the hydration water suppresses protein motions, albeit itself exhibiting a dynamical change around 180-190 K that seems to correspond to the glass transition of the protein. This suppression of protein motion seems to be stronger for GFP than for many other proteins, owing to its barrel-like shape. But at higher temperatures the hydration water has the opposite effect, enhancing protein dynamics. Here, however, at least on the ps-ns timescale probed, the hydration waters behave diffusively while the protein motions are confined to within 3 ångstroms or so.
In something of a companion piece, Jeremy and his coworkers again use neutron scattering and MD to probe protein dynamics, this time looking at the atomic motions in lysozyme at different levels of hydration on timescales from ps to ns (L. Hong et al., Phys. Rev. Lett. 108, 238102; 2012 – paper here). They ask whether the effect of hydration on protein motions is local to the interface or propagates into the protein core. Previously, hydration has tended to be considered in terms of its effect on conformational dynamics: how it changes the ability of protein atoms to jump between potential wells. But the researchers say that, on these timescales, the principal effect of hydration seems to be to enlarge the volume of the well within which protein atoms can diffuse locally. Nevertheless, because of strong coupling between such wells – I guess this means cooperativity of atomic motions – the effect can propagate into the protein interior and soften the whole molecule. Consistent with the Biophys. J. paper above, they observe the same kind of behaviour in GFP.
A very interesting new take on hydration is offered by Franci Merzel of the National Institute of Chemistry in Ljubljana and colleagues (Jeremy Smith is among these too – busy man) (A. Godec et al., Phys. Rev. Lett. 107, 267801; 2012 – paper here). Their MC simulations suggest that as a solute becomes more hydrophilic/polar, the hydration water tends to fractionate into a more highly ordered and less highly ordered component. This allows the former to rearrange its hydrogen-bonded network so that the bond angles are optimal, while the latter is released from the network. So while the hydration water of hydrophobic solutes is less orientationally flexible, it is NOT more tetrahedrally ordered, as is commonly thought; rather, hydration water of hydrophilic solutes is in fact more tetrahedral, on average, but there is less of it. In any event, say the authors, the picture is considerably more complex than any notions of ‘icebergs’ around hydrophobes.
Chang Sun at Nanyang Technological University in Singapore and his coworkers have been developing interesting ideas about how some of water’s properties can be rationalized by the differences between the covalent and hydrogen-bonded portions of the O-H-O links in the water network, in which Coulomb repulsion between the unevenly bound electron pairs can produce stiffening of the shorter covalent bond and softening and lengthening of the hydrogen bond. This idea is developed in a preprint (C. Sun et al., http://www.arxiv.org/abs/1210.1638) in which Sun and colleagues say that this effect can account for the stiffening of phonon modes in molecular clusters of water molecules, surface skins and ultrathin water films. The latter have been found to exhibit ice-like (or glue-like) properties and to be somewhat hydrophobic, as Haiping Fang and coworkers have reported (C. Wang et al., Phys. Rev. Lett. 103, 137801 (2009)).
Mihail Barboiu at the Institute Europeen des Membranes in Montpellier has reviewed some of the ways to make artificial water channels for bilayer membranes (Angew. Chem. Int. Ed. 51, 11674; 2012 – paper here), which are of course of great potential interest for water purification. This piece brought to my attention Mihail’s earlier work on channels made by the self-assembly of quartets of ureido imidazole molecules, which will stack into channels held together by hydrogen bonding to internal water wires and allow water and protons to permeate lipid bilayers (Y. Le Duc et al., Angew. Chem. Int. Ed. 50, 11366; 2011 – paper here).
The prevailing view of the hydration of small hydrophobes now seems to be that they are accommodated without a significant perturbation of water’s hydrogen-bonded network. This idea is supported by ab initio MD calculations of Fabio Sterpone at the Université Paris Diderot and his colleagues, who look at the hydration of methane (M. Montagna et al., J. Phys. Chem. B 116, 11695; 2012 – paper here). They say that the water molecules form a clathrate-like structure around the solute, although by this they do not imply anything static: the hydration shell is rather dynamic, and fails to produce any features in the IR spectrum significantly different from that of the bulk, although there are small signatures in the OH stretching and librational bands.
Steven Boxer at Stanford and colleagues have used time-resolved vibrational spectroscopy to examine the dynamics of water molecules in the active site of a ketosteroid isomerase (S. K. Jha et al., J. Phys. Chem. B 116, 11414; 2012 – paper here). They find that waters in the active site are much more rigid during the catalytic cycle than those in bulk, and suppose that this is by design rather than an epiphenomenon: the rigidified waters may help to preserve the particular electrostatic environment required for catalysis. In other words, catalysis here doesn’t provoke water ordering but is preceded and enabled by it.
Here’s an old(ish) paper of which I was recently made aware, in which water-assisted binding of a protein and ligand is dissected in detail by Alfonso García-Sosa at the University of Tartu in Estonia and Ricardo Mancera at the Curtin University of Technology in Australia (Mol. Informatics 29, 589; 2010 – paper here). Using MD simulations, they calculate the free-energy cost of removing the tightly bound water molecule from the SH3 domain of Ableson tyrosine kinase with several bound ligands (this molecule mediates protein-protein interactions), by adding functional groups to the peptide substrate that displace the water. They find that this process is unfavourable in all cases except for three substituents: hydroxyl, ethyl and formamide. The key point is in the methodology: the thermodynamics of such substitutions can be examined, and the role of the water assessed, with implications for drug design.
And here’s another paper that I missed last year. Lignin is one of the recalcitrant components in the conversion of biomass to biofuels, and pretreatments are needed in order to break down the lignin barrier that slows cellulose hydrolysis. Lignin is a hydrophobic polymer which is dense, aggregated and glassy in water at room temperature but softens and becomes more extended at higher temperatures. Jeremy Smith and colleagues have investigated the hydration changes that accompany this transition using MD simulations (L. Petridis et al., JACS 133, 20277; 2011 – paper here). They find that at high temperature (above about 420 K) the polymers form fractal crumpled globules, while the low-temperature collapse (around 300 K) is driven by density fluctuations of water removed from the hydration shell: the fluctuations in the bulk are slightly greater than those in the hydration shell, producing an entropic driving force for the collapse. Ultimately these insights might be of use for improving the efficiency of the pretreatment process.
How many water molecules does it take to make ice? Around 275 ± 25, according to Thomas Zeuch of the University of Göttingen and colleagues. Their IR spectra of size-selected water clusters show the first signs of crystallization, while the clear ice-like spectral feature of the 3200 cm-1 OH stretch is evident by clusters of around 475 molecules (C. C. Pradzynski et al., Science 337, 1529; 2012 – paper here). The researchers think it should be possible to follow the evolution of the cluster at least to sizes of around 1000 molecules, where one might begin to see bulk-like behaviour.
Considerably more to come. I have a long plane trip coming up, so you might get it soon.
In a second paper Jeremy, with Alexei Sokolov and coworkers, use neutron scattering to look at the dynamics of (fully deuterated) GFP and its hydration shell (J. D. Nickels et al., Biophys. J. 103, 1566-1575; 2012 – paper here). The interaction between solvent and solute dynamics is complex. At lower temperatures (below about 200 K) the hydration water suppresses protein motions, albeit itself exhibiting a dynamical change around 180-190 K that seems to correspond to the glass transition of the protein. This suppression of protein motion seems to be stronger for GFP than for many other proteins, owing to its barrel-like shape. But at higher temperatures the hydration water has the opposite effect, enhancing protein dynamics. Here, however, at least on the ps-ns timescale probed, the hydration waters behave diffusively while the protein motions are confined to within 3 ångstroms or so.
In something of a companion piece, Jeremy and his coworkers again use neutron scattering and MD to probe protein dynamics, this time looking at the atomic motions in lysozyme at different levels of hydration on timescales from ps to ns (L. Hong et al., Phys. Rev. Lett. 108, 238102; 2012 – paper here). They ask whether the effect of hydration on protein motions is local to the interface or propagates into the protein core. Previously, hydration has tended to be considered in terms of its effect on conformational dynamics: how it changes the ability of protein atoms to jump between potential wells. But the researchers say that, on these timescales, the principal effect of hydration seems to be to enlarge the volume of the well within which protein atoms can diffuse locally. Nevertheless, because of strong coupling between such wells – I guess this means cooperativity of atomic motions – the effect can propagate into the protein interior and soften the whole molecule. Consistent with the Biophys. J. paper above, they observe the same kind of behaviour in GFP.
A very interesting new take on hydration is offered by Franci Merzel of the National Institute of Chemistry in Ljubljana and colleagues (Jeremy Smith is among these too – busy man) (A. Godec et al., Phys. Rev. Lett. 107, 267801; 2012 – paper here). Their MC simulations suggest that as a solute becomes more hydrophilic/polar, the hydration water tends to fractionate into a more highly ordered and less highly ordered component. This allows the former to rearrange its hydrogen-bonded network so that the bond angles are optimal, while the latter is released from the network. So while the hydration water of hydrophobic solutes is less orientationally flexible, it is NOT more tetrahedrally ordered, as is commonly thought; rather, hydration water of hydrophilic solutes is in fact more tetrahedral, on average, but there is less of it. In any event, say the authors, the picture is considerably more complex than any notions of ‘icebergs’ around hydrophobes.
Chang Sun at Nanyang Technological University in Singapore and his coworkers have been developing interesting ideas about how some of water’s properties can be rationalized by the differences between the covalent and hydrogen-bonded portions of the O-H-O links in the water network, in which Coulomb repulsion between the unevenly bound electron pairs can produce stiffening of the shorter covalent bond and softening and lengthening of the hydrogen bond. This idea is developed in a preprint (C. Sun et al., http://www.arxiv.org/abs/1210.1638) in which Sun and colleagues say that this effect can account for the stiffening of phonon modes in molecular clusters of water molecules, surface skins and ultrathin water films. The latter have been found to exhibit ice-like (or glue-like) properties and to be somewhat hydrophobic, as Haiping Fang and coworkers have reported (C. Wang et al., Phys. Rev. Lett. 103, 137801 (2009)).
Mihail Barboiu at the Institute Europeen des Membranes in Montpellier has reviewed some of the ways to make artificial water channels for bilayer membranes (Angew. Chem. Int. Ed. 51, 11674; 2012 – paper here), which are of course of great potential interest for water purification. This piece brought to my attention Mihail’s earlier work on channels made by the self-assembly of quartets of ureido imidazole molecules, which will stack into channels held together by hydrogen bonding to internal water wires and allow water and protons to permeate lipid bilayers (Y. Le Duc et al., Angew. Chem. Int. Ed. 50, 11366; 2011 – paper here).
The prevailing view of the hydration of small hydrophobes now seems to be that they are accommodated without a significant perturbation of water’s hydrogen-bonded network. This idea is supported by ab initio MD calculations of Fabio Sterpone at the Université Paris Diderot and his colleagues, who look at the hydration of methane (M. Montagna et al., J. Phys. Chem. B 116, 11695; 2012 – paper here). They say that the water molecules form a clathrate-like structure around the solute, although by this they do not imply anything static: the hydration shell is rather dynamic, and fails to produce any features in the IR spectrum significantly different from that of the bulk, although there are small signatures in the OH stretching and librational bands.
Steven Boxer at Stanford and colleagues have used time-resolved vibrational spectroscopy to examine the dynamics of water molecules in the active site of a ketosteroid isomerase (S. K. Jha et al., J. Phys. Chem. B 116, 11414; 2012 – paper here). They find that waters in the active site are much more rigid during the catalytic cycle than those in bulk, and suppose that this is by design rather than an epiphenomenon: the rigidified waters may help to preserve the particular electrostatic environment required for catalysis. In other words, catalysis here doesn’t provoke water ordering but is preceded and enabled by it.
Here’s an old(ish) paper of which I was recently made aware, in which water-assisted binding of a protein and ligand is dissected in detail by Alfonso García-Sosa at the University of Tartu in Estonia and Ricardo Mancera at the Curtin University of Technology in Australia (Mol. Informatics 29, 589; 2010 – paper here). Using MD simulations, they calculate the free-energy cost of removing the tightly bound water molecule from the SH3 domain of Ableson tyrosine kinase with several bound ligands (this molecule mediates protein-protein interactions), by adding functional groups to the peptide substrate that displace the water. They find that this process is unfavourable in all cases except for three substituents: hydroxyl, ethyl and formamide. The key point is in the methodology: the thermodynamics of such substitutions can be examined, and the role of the water assessed, with implications for drug design.
And here’s another paper that I missed last year. Lignin is one of the recalcitrant components in the conversion of biomass to biofuels, and pretreatments are needed in order to break down the lignin barrier that slows cellulose hydrolysis. Lignin is a hydrophobic polymer which is dense, aggregated and glassy in water at room temperature but softens and becomes more extended at higher temperatures. Jeremy Smith and colleagues have investigated the hydration changes that accompany this transition using MD simulations (L. Petridis et al., JACS 133, 20277; 2011 – paper here). They find that at high temperature (above about 420 K) the polymers form fractal crumpled globules, while the low-temperature collapse (around 300 K) is driven by density fluctuations of water removed from the hydration shell: the fluctuations in the bulk are slightly greater than those in the hydration shell, producing an entropic driving force for the collapse. Ultimately these insights might be of use for improving the efficiency of the pretreatment process.
How many water molecules does it take to make ice? Around 275 ± 25, according to Thomas Zeuch of the University of Göttingen and colleagues. Their IR spectra of size-selected water clusters show the first signs of crystallization, while the clear ice-like spectral feature of the 3200 cm-1 OH stretch is evident by clusters of around 475 molecules (C. C. Pradzynski et al., Science 337, 1529; 2012 – paper here). The researchers think it should be possible to follow the evolution of the cluster at least to sizes of around 1000 molecules, where one might begin to see bulk-like behaviour.
Considerably more to come. I have a long plane trip coming up, so you might get it soon.
Thursday, October 18, 2012
Hydrophilic repulsion
I somehow missed a whole suite of papers in a special issue of PCCP (here) in 2010 on water in biological systems. I stumbled upon it the other day. There is too much there for me to work through every paper – suffice it to say that it covers topics ranging from water in the prebiotic evolution of DNA to water mediation of antifreeze proteins and anaesthetics, and is well worth a look.
The effort to understand hydrophobic attraction has rather overshadowed the study of interactions between hydrophilic surfaces – although, as Roland Netz and colleagues point out (E. Schneck et al., PNAS 109, 14405; 2012 – paper here), the repulsion between such surfaces, balancing out the van der Waals attraction, is ultimately what prevents biological matter from collapsing. This interaction is fairly well characterized for neutral phospholipid bilayers, but also acts between proteins, polysaccharides and nucleic acids, with exponential decay. All the same, the origins of the force, though evidently bound up with hydration, are not well understood. Netz and colleagues study it in this paper using MD simulations of zwitterionic lipid bilayers. Part of the repulsion comes from the reduction in configurational entropy of the head groups, but part is water-mediated and enthalpic, due to the expulsion of water bound to the head groups as the surfaces approach. However, at separations that allow at least 17 water molecules to hydrate each head group, the water-mediated repulsion becomes dominated by an entropic effect due to the alignment of water dipoles: at smaller separations, there is depolarization due to frustration in the dipole orientations of water molecules close to each of the two surfaces. In other words, the repulsive interaction is complex, subtle and finely tuned.
I recently saw Veronica Vaida talk about the catalytic potential of the air-water interface as a hydrophobic environment that can enhance the condensation reaction of peptide bond formation. She and Elizabeth Griffith now offer experimental support for that notion (PNAS 109, 15697; 2012 – paper here). They report IR spectroscopic evidence that leucine, as an ethyl ester, will partition to the air-water interface in a Langmuir trough, coordinate there to copper(II) ions, and undergo condensation to form peptide bonds. The prebiotic implications are clear, offering yet another reason to be interested in what goes on at this ubiquitous interface.
Alfonso De Simone at Imperial College and coworkers have investigated a nice model system for ligand binding in protein cavities: macrocyclic cucurbituril molecules, which bind a variety of hydrophobic guests very strongly (F. Biedermann et al., JACS 134, 15318; 2012 – paper here). Their simulations indicate that release of “high-energy” water in the cavity is a major driving force of binding, being favourable both enthalpically and entropically. I see that a similar conclusion is reached by C. N. Nguyen et al. in J. Chem. Phys. 137, 044101 (2012), a paper I’ve not seen beyond the abstract but which also shows that a high water density can be achieved inside these cavities despite the absence of strong solvent-cavity interactions. The paper is here.
Bob Eisenberg at Rush University and coworkers use a variational theory to probe the energetics of ion flow through protein channels (T.-L. Horng et al., J. Phys. Chem. B 116, 11422; 2012 – paper here). They say that this approach captures the electrostatic interactions that classical theories of such channels tend to ignore in their assumption of ideality of the ionic solutions. Bob’s papers always seem to contain some pungent and pertinent general comments that makes them thought-provoking (and fun) to read, viz.
“Early workers of some reputation in molecular biology, including Nobel Prize winners, attributed the secret of life to allosteric interactions of chemical signals acting on proteins and then channels. It is striking to the biologists among us that a self-consistent model of ions and side chains in channels produces strong interactions over long distances (i.e., more than 1 nm) without invoking the metaphors of vitalistic allostery. The calculations of a self-consistent variational theory of the energetics of complex fluids seem ready to replace the poetry of our ancestors… It is amusing that physicists learned to use self-consistent mathematics to analyze (control and build) complex interacting systems of holes and electrons during the same years that biologists used poetry to describe complex interacting systems of cations and anions… Certainly, a theoretical and computational approach to biology and its molecules must allow everything to interact with everything else, instead of assuming that everything is ideal and nothing interacts with nothing.”
I encountered hyaluronan recently as a polysaccharide important for the integrity of the extracellular matrix, and thus involved in skin ageing. Hydration of this macromolecule is therefore of considerable interest for skin cosmetics. Johannes Hunger at FOM Amsterdam and colleagues have used ultrafast IR and THz spectroscopy to investigate the dynamics of its hydration shell in solution, and find that around 15 waters per disaccharide unit are significantly slowed in terms of their reorientiation – a figure comparable to that found for other polysaccharides, such as dextran (J. Hunger et al., Biophys. J. 103, L10; 2012 – paper here).
A study of zwitterionic amino-acid hydration by Inigo Rodríguez-Arteche and colleagues at the University of País Vasco in San Sebastian, Spain, indicates that, despite their large dipole moments, these ions are very well screened by water and show little tendency for dipolar alignment at moderate concentrations (I. Rodríguez-Arteche et al., Phys. Chem. Chem. Phys. 14, 11352; 2012 – paper here). Again, and insurprisingly, the dielectric spectroscopic measurements reported here show significant slowing of water dynamics in the hydration shells.
Techniques I have never heard of before have been used by Mark Chance at Case Western Reserve and coworkers to study the structure and dynamics of protein-bound waters (S. Gupta et al., PNAS 109, 14882; 2012 – paper here). I don’t fully understand these methods, but they involve radiolytic formation of hydroxyl radicals at the protein surface, followed by diffusion of the radicals to reactive sites on the proteins and then identification by mass spectrometry. If this radiolytic method is used in O-18-enriched water, it results in selective O-18 labelling of certain residues. Time-resolved studies of O-16/O-18 exchange can then give information about water-exchange dynamics in the hydration shell. These techniques can apparently give information about the water-exchange rates for specific residues in an active-site pocket – the cases studied here are cytochrome c and ubiquitin.
I enjoyed the RSC Faraday Discussion on Hofmeister Effects in September; I gather that the proceedings will appear quite shortly, judging by the speed at which the papers were prepared. A further small advert: I have written a chapter on water in the forthcoming book Physical Chemistry in Action: Astrochemistry and Astrobiology, edited by Ian Smith, Sydney Leach and Charles Cockell and published by Springer in early November - see here.
For those who have sent me papers not mentioned here – they will be soon. I’m just getting some older things cleared first. Please do keep sending them.
The effort to understand hydrophobic attraction has rather overshadowed the study of interactions between hydrophilic surfaces – although, as Roland Netz and colleagues point out (E. Schneck et al., PNAS 109, 14405; 2012 – paper here), the repulsion between such surfaces, balancing out the van der Waals attraction, is ultimately what prevents biological matter from collapsing. This interaction is fairly well characterized for neutral phospholipid bilayers, but also acts between proteins, polysaccharides and nucleic acids, with exponential decay. All the same, the origins of the force, though evidently bound up with hydration, are not well understood. Netz and colleagues study it in this paper using MD simulations of zwitterionic lipid bilayers. Part of the repulsion comes from the reduction in configurational entropy of the head groups, but part is water-mediated and enthalpic, due to the expulsion of water bound to the head groups as the surfaces approach. However, at separations that allow at least 17 water molecules to hydrate each head group, the water-mediated repulsion becomes dominated by an entropic effect due to the alignment of water dipoles: at smaller separations, there is depolarization due to frustration in the dipole orientations of water molecules close to each of the two surfaces. In other words, the repulsive interaction is complex, subtle and finely tuned.
I recently saw Veronica Vaida talk about the catalytic potential of the air-water interface as a hydrophobic environment that can enhance the condensation reaction of peptide bond formation. She and Elizabeth Griffith now offer experimental support for that notion (PNAS 109, 15697; 2012 – paper here). They report IR spectroscopic evidence that leucine, as an ethyl ester, will partition to the air-water interface in a Langmuir trough, coordinate there to copper(II) ions, and undergo condensation to form peptide bonds. The prebiotic implications are clear, offering yet another reason to be interested in what goes on at this ubiquitous interface.
Alfonso De Simone at Imperial College and coworkers have investigated a nice model system for ligand binding in protein cavities: macrocyclic cucurbituril molecules, which bind a variety of hydrophobic guests very strongly (F. Biedermann et al., JACS 134, 15318; 2012 – paper here). Their simulations indicate that release of “high-energy” water in the cavity is a major driving force of binding, being favourable both enthalpically and entropically. I see that a similar conclusion is reached by C. N. Nguyen et al. in J. Chem. Phys. 137, 044101 (2012), a paper I’ve not seen beyond the abstract but which also shows that a high water density can be achieved inside these cavities despite the absence of strong solvent-cavity interactions. The paper is here.
Bob Eisenberg at Rush University and coworkers use a variational theory to probe the energetics of ion flow through protein channels (T.-L. Horng et al., J. Phys. Chem. B 116, 11422; 2012 – paper here). They say that this approach captures the electrostatic interactions that classical theories of such channels tend to ignore in their assumption of ideality of the ionic solutions. Bob’s papers always seem to contain some pungent and pertinent general comments that makes them thought-provoking (and fun) to read, viz.
“Early workers of some reputation in molecular biology, including Nobel Prize winners, attributed the secret of life to allosteric interactions of chemical signals acting on proteins and then channels. It is striking to the biologists among us that a self-consistent model of ions and side chains in channels produces strong interactions over long distances (i.e., more than 1 nm) without invoking the metaphors of vitalistic allostery. The calculations of a self-consistent variational theory of the energetics of complex fluids seem ready to replace the poetry of our ancestors… It is amusing that physicists learned to use self-consistent mathematics to analyze (control and build) complex interacting systems of holes and electrons during the same years that biologists used poetry to describe complex interacting systems of cations and anions… Certainly, a theoretical and computational approach to biology and its molecules must allow everything to interact with everything else, instead of assuming that everything is ideal and nothing interacts with nothing.”
I encountered hyaluronan recently as a polysaccharide important for the integrity of the extracellular matrix, and thus involved in skin ageing. Hydration of this macromolecule is therefore of considerable interest for skin cosmetics. Johannes Hunger at FOM Amsterdam and colleagues have used ultrafast IR and THz spectroscopy to investigate the dynamics of its hydration shell in solution, and find that around 15 waters per disaccharide unit are significantly slowed in terms of their reorientiation – a figure comparable to that found for other polysaccharides, such as dextran (J. Hunger et al., Biophys. J. 103, L10; 2012 – paper here).
A study of zwitterionic amino-acid hydration by Inigo Rodríguez-Arteche and colleagues at the University of País Vasco in San Sebastian, Spain, indicates that, despite their large dipole moments, these ions are very well screened by water and show little tendency for dipolar alignment at moderate concentrations (I. Rodríguez-Arteche et al., Phys. Chem. Chem. Phys. 14, 11352; 2012 – paper here). Again, and insurprisingly, the dielectric spectroscopic measurements reported here show significant slowing of water dynamics in the hydration shells.
Techniques I have never heard of before have been used by Mark Chance at Case Western Reserve and coworkers to study the structure and dynamics of protein-bound waters (S. Gupta et al., PNAS 109, 14882; 2012 – paper here). I don’t fully understand these methods, but they involve radiolytic formation of hydroxyl radicals at the protein surface, followed by diffusion of the radicals to reactive sites on the proteins and then identification by mass spectrometry. If this radiolytic method is used in O-18-enriched water, it results in selective O-18 labelling of certain residues. Time-resolved studies of O-16/O-18 exchange can then give information about water-exchange dynamics in the hydration shell. These techniques can apparently give information about the water-exchange rates for specific residues in an active-site pocket – the cases studied here are cytochrome c and ubiquitin.
I enjoyed the RSC Faraday Discussion on Hofmeister Effects in September; I gather that the proceedings will appear quite shortly, judging by the speed at which the papers were prepared. A further small advert: I have written a chapter on water in the forthcoming book Physical Chemistry in Action: Astrochemistry and Astrobiology, edited by Ian Smith, Sydney Leach and Charles Cockell and published by Springer in early November - see here.
For those who have sent me papers not mentioned here – they will be soon. I’m just getting some older things cleared first. Please do keep sending them.
Monday, August 20, 2012
Making sense of Hofmeister
In preparation for the forthcoming RSC Faraday Discussion on Hofmeister effects, Pavel Jungwirth, Paul Cremer and their coworkers describe how certain ion-specific interactions with peptides occur (K. B. Rembert et al., JACS ja301297g – paper here). They have looked both experimentally (NMR, thermodynamic measurements) and with MD at the interaction of anions such as iodide, sulphate, chloride and thiocyanate with a model 600-residue elastin-like peptide. Large, soft and weakly hydrated anions such as I- and SCN- bind to an amide nitrogen and the adjacent alpha-carbon, where there is a slight positive charge, promoting peptide solubility and disrupting peptide-water hydrogen bonds. However, at higher concentrations, saturation of these binding sites can eventually lead to salting out because the anions then increase the surface tension of purely hydrophobic portions of the peptide-water interface. In contrast, chloride, further up the Hofmeister series, binds only weakly at these sites, while sulphate, further up still, is repelled from them. The work shows once again how the Hofmeister behaviour is determined by direct interactions between the ions and peptide.
Paul Cremer and colleagues have also considered how carboxylate side-chain groups in a peptide affect Hofmeister cationic effects (J. Kherb et al., J. Phys. Chem. B 116, 7389; 2012 – paper here). These ions will interact directly with the carboxylates to form ion pairs. The influence of the monovalent cations is generally consistent with the ‘law of matching water affinity’, which posits that anions and cations of similar hydration energies will preferentially form ion pairs. One exception here is ammonium, which can form hydrogen bonds with carboxylate. Lithium is also anomalous, perhaps because its tight binding of water leads to the formation of an ion pair mediated by shared waters rather than via direct contacts.
More on Hofmeister effects comes from Juan Luis Ortega-Vinuesa at the University of Granada and colleagues, who look at ion-specific effects in colloidal interactions, specifically on the aggregation of hydrophobic particles (polystyrene nanobeads) (T. López-León et al., ChemPhysChem 13, 2382; 2012 – paper here). They find that anions early in the series (sulphate, chloride) behave in accord with the predictions of DLVO theory, but large, polarizable anions (nitrate, thiocyanate) do not. The (fractal) morphology of the aggregates also differs for different ions. The findings are intriguing, but the suggested interpretation in terms of ion effects on ‘water structure’ is indirect (as the authors acknowledge) and, I think, open to debate.
Enzymes can become inactivated by covalent binding in the active site, a process known as mechanism-based inactivation, which can have important physiological consequences. Hajime Hirao and colleagues at Nanyang Technological University in Singapore have investigated how this occurs for cytochrome P450, which can for example be inactivated by acetylenes (J. Phys. Chem. B jp302592d – paper here). Their density-functional theory calculations suggest that the reaction is mediated by a catalytic water molecule in the binding site, which donates a proton to the acetylene group.
Do the various types of denaturation of proteins share any common features? Cristiano Dias of the Free University of Berlin suggests a unifying picture of cold and pressure denaturation that involves solvation of nonpolar residues by a monolayer or so of water (Phys. Rev. Lett. 109, 048104; 2012 – paper here). Because these solvated states have a lower volume and H-bond free energy than others, they are favoured at high pressure and at low temperature. Using this picture in a very simple bead-spring model of folded proteins, with water described by the two-dimensional Mercedes-Benz model, Dias can reproduce the ellipsoidal NPT phase diagram of proteins.
Pablo Debenedetti at Princeton and his coworkers have been exploring much the same issues using another simple model: a lattice model of homo- and heteropolymers in two and three dimensions (e.g. Patel et al., J. Chem. Phys. 128, 175102 (2008) and Matysiak et al., J. Phys. Chem. B 10/1021/jp3039175 (2012)). They now show that a hydrophobic polymer in the 3D system (with tetrahedral water), which adopts a collapsed conformation within a certain temperature range, will undergo both thermal denaturation and cold denaturation above and below this regime (S. R.-V. Castrillón et al., J. Phys. Chem. B jp3039237 – paper here). The mechanisms of denaturation are distinct at high and low temperatures: the former is an extended random coil, while the latter is still relatively compact but strongly water-penetrated.
The role of small-molecule denaturants is also becoming steadily more clear. Ruhong Zhou at IBM Yorktown Heights, working with colleagues in Hangzhou, has looked at whether the direct-interaction mechanism of destabilization seen previously for lysozyme (Hua et al., PNAS 105, 16928; 2008) applies also to other proteins and peptides (Z. Yang et al., J. Phys. Chem. B jp304114h – paper here). They find that indeed urea seems to act in the same way here, via direct dispersion interactions with the peptide, rather than due to ‘structure-breaking’ effects on water.
The stability of biological macromolecules under conditions which mimic those of the intracellular environment, rich in cosolutes and subject to crowding, has become a focus of increasing attention. Shu-ichi Nakano and colleagues at Konan University in Kobe have investigated the hydration and conformational stability of DNA hairpin oligonucleotides under such conditions, specifically in the presence of PEG and other alcohols (Biophys. J. 102, 2808; 2012 – paper here). They find that aliphatic alcohol cosolutes decrease the stability of base-pair interactions, and may also destabilize the hairpins when the alcohols have fewer hydroxyl groups. In general it appears that binding of water molecules to DNA is promoted by structural order in the oligonucleotide.
Proton transport in many proton channels is believed to happen via hopping along a chain of hydrogen-bonded water molecules. This process in gramicidin A is studied by MD simulations, in particular to model the 2D infrared spectra of amide C=O stretches, by Jasper Knoester and colleagues at the University of Groningen (C. Liang et al., J. Phys. Chem. B 116, 6336; 2012 – paper here). They find that smearing of the isotope-labelled spectra seems to result from cooperativity of proton hopping and water rotation in the channel.
Water in protein channels is also the subject of a preprint from Diego Prada-Gracia and Francesco Rao at the Freibrug Institute for Advanced Studies (arxiv:1207.6953; paper here). They consider how a water molecule in the pore of a potassium channel (KcsA) affects the selectivity. In the presence of water, the equilibrium position for a sodium ion in the channel is shifted relative to the position both it and potassium occupy in a water-free channel. Such a water molecule does not actually enter the pore in the case of potassium – waters instead stay only outside, but close to, the pore entrance and exit, interacting more weakly with the ion inside. Thus the channel is able to bind both ions but on a quite different structural basis, with implications for its selectivity.
Three papers on hydration of small molecules: hydrophobic, the other hydrophilic. John Tatini Titantah and Mikko Karttunen at the Universities of Western Ontario and Waterloo respectively have performed first-principles MD simulations of the hydration of tetramethylurea with a view to testing the old ‘iceberg’ picture of Frank and Evans (JACS 134, 9362; 2012 – paper here). They note that while femtosecond IR measurements by Rezus and Bakker indicate a slowing of water dynamics in the hydration shell of hydrophobes (Phys. Rev. Lett. 99, 148301; 2007), Qvist and Halle recently found in contrast that the dynamics revealed by NMR are faster than the bulk (JACS 130, 10345; 2008). The authors here do find that some (but by no means all) of the hydration waters of TMU are slowed, and that some have a long residence time in the hydration shell. That would seem to support Rezus and Bakker, but unless I missed it, I can’t find an explanation for the discrepancy with the NMR results.
In the second paper, Laura Lupi at the Università degli Studi di Perugia and colleagues have used MD simulations to disentangle the dynamics of water molecules in the hydration sphere of trehalose from those in the bulk, clarifying the two dynamical populations revealed by light-scattering experiments (J. Phys. Chem. B 116, 7499; 2012 – paper here). They find that waters in the first hydration shell are retarded by a factor of about 5, while beyond this there is little significant perturbation of the dynamics relative to the bulk.
In contrast, an oxygen-17 NMR spin relaxation study of trehalose hydration by Bertil Halle and colleagues at Lund shows more modest perturbation of hydration water, with the rotation rates slowed only by a factor of around 1.6 in the first hydration shell (L. R. Winther et al., J. Phys. Chem. B jp304982c – paper here). They agree, however, that any effect on waters beyond this first shell is negligible. Moreover, these authors report significant clustering of the solute, which may or may not be linked to trehalose’s protein-stabilizing influence.
I believe I’ve mentioned previously work by Martin Weik at Grenoble and colleagues on the hydration of intrinsically disordered proteins, and how, by comparing folded globular and membrane proteins, the authors conclude that there is a gradient in the coupling between the dynamics of a protein and its hydration water that depends on the degree of intrinsic structure in the protein. In any event, it is now published (F.-X. Gallat et al., Biophys. J. 103, 129; 2012 – paper here). Using elastic incoherent neutron scattering, the authors find that the coupling seems to decline from a high value for these disordered proteins to more moderate coupling for globular proteins and then weak coupling for membrane proteins. As they put it, “A coherent picture thus emerges in which hydration water, rather than being a mere epiphenomenon, is an integral part of the biologically active protein.”
Teresa Head-Gordon at Berkeley and colleagues have devised a method for optimizing water-solute van der Waals interactions so as to accurately reproduce experimental small-peptide solvation energies in force-field calculations (P. S. Nerenberg et al., J. Phys. Chem. B 116, 4524; 2012 – paper here). Meanwhile, Wilfred van Gunsteren and colleagues at ETH present a coarse-grained water model that reproduces hydration behaviour of proteins at low computational cost (S. Riniker et al., J. Phys. Chem. B jp304188z – paper here). This entails the inclusion of a 0.8 nm later of atomistic water to capture hydrogen-bonding interactions with the protein while allowing only for coarse-graining beyond this – speeding up simulation times by about an order of magnitude.
The merits of the many water models currently in use, such as SPC, TIP4P, TIP5P etc, are much debated. Francesco Rao and coworkers at the University of Freiburg show that all seven widely used models produce the same hydrogen-bonding topology of water, albeit somewhat shifted to differing temperatures (R. Shevchuk et al., J. Phys. Chem. B 116, 7538; 2012 – paper here). The full microscopic geometry and radial distribution functions are not, however, identical in all cases.
Paul Cremer and colleagues have also considered how carboxylate side-chain groups in a peptide affect Hofmeister cationic effects (J. Kherb et al., J. Phys. Chem. B 116, 7389; 2012 – paper here). These ions will interact directly with the carboxylates to form ion pairs. The influence of the monovalent cations is generally consistent with the ‘law of matching water affinity’, which posits that anions and cations of similar hydration energies will preferentially form ion pairs. One exception here is ammonium, which can form hydrogen bonds with carboxylate. Lithium is also anomalous, perhaps because its tight binding of water leads to the formation of an ion pair mediated by shared waters rather than via direct contacts.
More on Hofmeister effects comes from Juan Luis Ortega-Vinuesa at the University of Granada and colleagues, who look at ion-specific effects in colloidal interactions, specifically on the aggregation of hydrophobic particles (polystyrene nanobeads) (T. López-León et al., ChemPhysChem 13, 2382; 2012 – paper here). They find that anions early in the series (sulphate, chloride) behave in accord with the predictions of DLVO theory, but large, polarizable anions (nitrate, thiocyanate) do not. The (fractal) morphology of the aggregates also differs for different ions. The findings are intriguing, but the suggested interpretation in terms of ion effects on ‘water structure’ is indirect (as the authors acknowledge) and, I think, open to debate.
Enzymes can become inactivated by covalent binding in the active site, a process known as mechanism-based inactivation, which can have important physiological consequences. Hajime Hirao and colleagues at Nanyang Technological University in Singapore have investigated how this occurs for cytochrome P450, which can for example be inactivated by acetylenes (J. Phys. Chem. B jp302592d – paper here). Their density-functional theory calculations suggest that the reaction is mediated by a catalytic water molecule in the binding site, which donates a proton to the acetylene group.
Do the various types of denaturation of proteins share any common features? Cristiano Dias of the Free University of Berlin suggests a unifying picture of cold and pressure denaturation that involves solvation of nonpolar residues by a monolayer or so of water (Phys. Rev. Lett. 109, 048104; 2012 – paper here). Because these solvated states have a lower volume and H-bond free energy than others, they are favoured at high pressure and at low temperature. Using this picture in a very simple bead-spring model of folded proteins, with water described by the two-dimensional Mercedes-Benz model, Dias can reproduce the ellipsoidal NPT phase diagram of proteins.
Pablo Debenedetti at Princeton and his coworkers have been exploring much the same issues using another simple model: a lattice model of homo- and heteropolymers in two and three dimensions (e.g. Patel et al., J. Chem. Phys. 128, 175102 (2008) and Matysiak et al., J. Phys. Chem. B 10/1021/jp3039175 (2012)). They now show that a hydrophobic polymer in the 3D system (with tetrahedral water), which adopts a collapsed conformation within a certain temperature range, will undergo both thermal denaturation and cold denaturation above and below this regime (S. R.-V. Castrillón et al., J. Phys. Chem. B jp3039237 – paper here). The mechanisms of denaturation are distinct at high and low temperatures: the former is an extended random coil, while the latter is still relatively compact but strongly water-penetrated.
The role of small-molecule denaturants is also becoming steadily more clear. Ruhong Zhou at IBM Yorktown Heights, working with colleagues in Hangzhou, has looked at whether the direct-interaction mechanism of destabilization seen previously for lysozyme (Hua et al., PNAS 105, 16928; 2008) applies also to other proteins and peptides (Z. Yang et al., J. Phys. Chem. B jp304114h – paper here). They find that indeed urea seems to act in the same way here, via direct dispersion interactions with the peptide, rather than due to ‘structure-breaking’ effects on water.
The stability of biological macromolecules under conditions which mimic those of the intracellular environment, rich in cosolutes and subject to crowding, has become a focus of increasing attention. Shu-ichi Nakano and colleagues at Konan University in Kobe have investigated the hydration and conformational stability of DNA hairpin oligonucleotides under such conditions, specifically in the presence of PEG and other alcohols (Biophys. J. 102, 2808; 2012 – paper here). They find that aliphatic alcohol cosolutes decrease the stability of base-pair interactions, and may also destabilize the hairpins when the alcohols have fewer hydroxyl groups. In general it appears that binding of water molecules to DNA is promoted by structural order in the oligonucleotide.
Proton transport in many proton channels is believed to happen via hopping along a chain of hydrogen-bonded water molecules. This process in gramicidin A is studied by MD simulations, in particular to model the 2D infrared spectra of amide C=O stretches, by Jasper Knoester and colleagues at the University of Groningen (C. Liang et al., J. Phys. Chem. B 116, 6336; 2012 – paper here). They find that smearing of the isotope-labelled spectra seems to result from cooperativity of proton hopping and water rotation in the channel.
Water in protein channels is also the subject of a preprint from Diego Prada-Gracia and Francesco Rao at the Freibrug Institute for Advanced Studies (arxiv:1207.6953; paper here). They consider how a water molecule in the pore of a potassium channel (KcsA) affects the selectivity. In the presence of water, the equilibrium position for a sodium ion in the channel is shifted relative to the position both it and potassium occupy in a water-free channel. Such a water molecule does not actually enter the pore in the case of potassium – waters instead stay only outside, but close to, the pore entrance and exit, interacting more weakly with the ion inside. Thus the channel is able to bind both ions but on a quite different structural basis, with implications for its selectivity.
Three papers on hydration of small molecules: hydrophobic, the other hydrophilic. John Tatini Titantah and Mikko Karttunen at the Universities of Western Ontario and Waterloo respectively have performed first-principles MD simulations of the hydration of tetramethylurea with a view to testing the old ‘iceberg’ picture of Frank and Evans (JACS 134, 9362; 2012 – paper here). They note that while femtosecond IR measurements by Rezus and Bakker indicate a slowing of water dynamics in the hydration shell of hydrophobes (Phys. Rev. Lett. 99, 148301; 2007), Qvist and Halle recently found in contrast that the dynamics revealed by NMR are faster than the bulk (JACS 130, 10345; 2008). The authors here do find that some (but by no means all) of the hydration waters of TMU are slowed, and that some have a long residence time in the hydration shell. That would seem to support Rezus and Bakker, but unless I missed it, I can’t find an explanation for the discrepancy with the NMR results.
In the second paper, Laura Lupi at the Università degli Studi di Perugia and colleagues have used MD simulations to disentangle the dynamics of water molecules in the hydration sphere of trehalose from those in the bulk, clarifying the two dynamical populations revealed by light-scattering experiments (J. Phys. Chem. B 116, 7499; 2012 – paper here). They find that waters in the first hydration shell are retarded by a factor of about 5, while beyond this there is little significant perturbation of the dynamics relative to the bulk.
In contrast, an oxygen-17 NMR spin relaxation study of trehalose hydration by Bertil Halle and colleagues at Lund shows more modest perturbation of hydration water, with the rotation rates slowed only by a factor of around 1.6 in the first hydration shell (L. R. Winther et al., J. Phys. Chem. B jp304982c – paper here). They agree, however, that any effect on waters beyond this first shell is negligible. Moreover, these authors report significant clustering of the solute, which may or may not be linked to trehalose’s protein-stabilizing influence.
I believe I’ve mentioned previously work by Martin Weik at Grenoble and colleagues on the hydration of intrinsically disordered proteins, and how, by comparing folded globular and membrane proteins, the authors conclude that there is a gradient in the coupling between the dynamics of a protein and its hydration water that depends on the degree of intrinsic structure in the protein. In any event, it is now published (F.-X. Gallat et al., Biophys. J. 103, 129; 2012 – paper here). Using elastic incoherent neutron scattering, the authors find that the coupling seems to decline from a high value for these disordered proteins to more moderate coupling for globular proteins and then weak coupling for membrane proteins. As they put it, “A coherent picture thus emerges in which hydration water, rather than being a mere epiphenomenon, is an integral part of the biologically active protein.”
Teresa Head-Gordon at Berkeley and colleagues have devised a method for optimizing water-solute van der Waals interactions so as to accurately reproduce experimental small-peptide solvation energies in force-field calculations (P. S. Nerenberg et al., J. Phys. Chem. B 116, 4524; 2012 – paper here). Meanwhile, Wilfred van Gunsteren and colleagues at ETH present a coarse-grained water model that reproduces hydration behaviour of proteins at low computational cost (S. Riniker et al., J. Phys. Chem. B jp304188z – paper here). This entails the inclusion of a 0.8 nm later of atomistic water to capture hydrogen-bonding interactions with the protein while allowing only for coarse-graining beyond this – speeding up simulation times by about an order of magnitude.
The merits of the many water models currently in use, such as SPC, TIP4P, TIP5P etc, are much debated. Francesco Rao and coworkers at the University of Freiburg show that all seven widely used models produce the same hydrogen-bonding topology of water, albeit somewhat shifted to differing temperatures (R. Shevchuk et al., J. Phys. Chem. B 116, 7538; 2012 – paper here). The full microscopic geometry and radial distribution functions are not, however, identical in all cases.
Tuesday, June 19, 2012
Hot spots and cavities
Ariel Fernández is developing a picture of biomolecular hydration that might be considered to make it analogous to the standard picture of liquid-solid interfaces in terms of surface free energy. That’s to say, he defines a measure called the epistructural interfacial tension (EIT) which plays the role of a kind of surface tension for proteins in water, being increased where hydration is imperfect (that is, where hydration water molecules have a reduced number of hydrogen-bond contacts) relative to the bulk. This EIT can then be considered to promote protein-protein associations where this can lower the total free energy, via hot spots on the protein surface where the EIT is elevated: regions of high surface free energy, you might say. Ariel has developed this notion previously (Proc. R. Soc. A 467, 559; 2011), and in a new paper (Phys. Rev. Lett. 108, 188102; 2012 – paper here) he explains how to derive the ‘water coordination field’ around a solute particle that minimizes the EIT. This reduces to the macroscopic surface tension in the large-curvature limit. Hot spots for protein association correspond to those positions on the surface that reduce the EIT most significantly on binding.
I have seen few more striking examples of the involvement of ‘structured’ hydration water in enzyme action than that supplied by Ursula Rothlisberger at EPFL in Lausanne and colleagues (E. Brunk et al., JACS 134, 8608; 2012 – paper here). They use classical and quantum MD to look at the mechanism of the DNA-repair enzyme MutY, which excises a DNA base damaged by hydroxyl radical oxidation. The first (rate-determining) step of the process involves protonation of the N7 of adenine, which is assisted by a highly organized catalytic cluster of five water molecules, as shown here. The authors suggest that the particular arrangement of hydrophobic and hydrophilic residues around the water cluster act as a ‘water trap’ to ensure that these waters have long residence times.
How hydration influences and perhaps dictates pressure- and cold-induced protein denaturation has been much studied, but is still in debate. Payel Das of IBM Yorktown Heights and Silvina Matysiak of the University of Maryland shed some light on this question with MD simulations of the denaturation of a model 32-mer hydrophobic polymer (J. Phys. Chem. B jp211832c – paper here). They find that folding to the compact state happens via a hairpin-like configuration with a vapour bubble at the elbow, and that high pressure suppresses this process by reducing water fluctuations – observations that seem rather consistent with the current view of dewetting-induced hydrophobic collapse. Cold, meanwhile, leads to enhanced tetrahedral ordering of the hydration shell, which also suppresses the collapse.
Ah, but here’s the thing: cavities – or if you like, vapour bubbles – inside a protein have been generally found to be destabilizing, tending to induce denaturation, as discussed in a Commentary article in PNAS by Brian Matthews of the University of Oregon (PNAS 10.1073/pnas.1204795109 – paper here). This piece is motivated by a paper by Roche et al. (PNAS 109, 6945; 2012 – paper here) looking at the influence of cavities on pressure denaturation, specifically on the pressure-induced unfolding of SNase mutants that have appreciable dry cavities in their interiors. They find that the cavities play a dominant role in the unfolding process via the reduction in protein volume on denaturation.
The coupling of protein and hydration-shell dynamics is the subject of a paper by Jeremy Smith and colleagues at Oak Ridge (L. Hong et al., Phys. Rev. Lett. 108, 238102; 2012 – paper here). They follow the dynamics up to ns timescales in MD simulations and neutron-scattering measurements of lysozyme, and find that the protein dynamics can be decomposed into three components: diffusion within a local potential well, methyl rotations and nonmethyl ‘jumps’ – which I take to be jumps of localized diffusional chain motion from one potential well to another. Hydration seems to increase the probability of these latter jumps, but it also broadens the volume accessible for localized diffusion – in effect making the protein ‘softer’. Moreover, this effect propagates from the solvent-accessible surface deep into the ‘dry’ protein interior, loosening up the entire molecule.
Coupling of hydration dynamics is also the topic of a study by Kevin Kubarych and colleagues at the University of Michigan (J. T. King et al., J. Phys. Chem. B jp300835k – paper here). They use ultrafast IR spectroscopy to probe water dynamics near the surface of two variants of lysozyme. As previous studies have indicated, these dynamics are highly heterogeneous in space, and can vary from bulk-like to highly retarded, the latter being found at extended hydrophobic surfaces and being due to reduced hydrogen-bonding exchange. Using solvent-exchange, they also find that the liberation of this water drives the association of small molecules (and by extension, perhaps other proteins) at the hydrophobic protein surfaces.
Bridging water molecules often play an important catalytic role in receptor-substrate interactions. But not, it seems, in the mechanism of threonyl-tRNA synthetase: James Gauld of the University of Windsor in Canada and colleagues show that, contrary to previous suggestions, a water molecule here seem to serve no useful role, but only disrupts the process (E. A. C. Bushnell et al., J. Phys. Chem. B 116, 5205; 2012 – paper here).
The effect of progressive hydration of a protein from an essentially dry state is studied by Oleg Boyarkin and colleagues at EPFL in Lausanne (N. S. Nagornova et al., Science 336, 320; 2012 – paper here). They form gas-phase clusters of the macrocyclic peptide gramicidin S complexed with various numbers of water molecules, from 1 to 50, and characterize the interactions using vibrational spectroscopy to monitor hydrogen-bonding. The effect of progressive hydration is most pronounced for the first two water molecules, which disrupt intramolecular non-covalent (amine cation to pi) bonds and cause significant elongation of the peptide, bringing it into a conformation close to that of the fully hydrated state.
An interesting preprint on dewetting-induced hydrophobic attraction by Naiyin Yu and Michael Hagan at Brandeis (arxiv:1206.1828 – paper here). The latest view of this picture (see Patel et al., J. Phys. Chem. B 116, 2498 (2012) – Hagan is a coauthor of this paper) posits that proteins that self-assemble via hydrophobic interactions tend to sit close to a dewetting transition, which – if it doesn’t happen spontaneously – might therefore be induced by small perturbations. Yu and Hagan support this idea with simulations of the dimerization of the HIV capsid protein. While the wild-type subunits assemble only by gradual expulsion of water, mutations enacted in silico to replace three hydrophilic residues at the interface with hydrophobic ones can trigger dewetting – and moreover that they do so in a way that reveals the cooperativity of drying and the sensitivity to surface topography. As the authors argue, “Since the CA-C dimerization interface is typical of protein binding surfaces, our results raise the possibility that many proteins sit near a dewetting transition”.
A simple model of the hydration of a hydrophobic particle is presented by Ken Dill of Stony Brook and colleagues in Ljubljana (M. Luksic et al., J. Phys. Chem. B 116, 6177; 2012 – paper here). The model is two-dimensional, with water molecules modelled as ‘Mercedes Benz’ circular particles that engage in trigonal hydrogen bonding – simple enough to be solved almost analytically. The aim here is to probe the effects of hydrogen bonding and van der Waals interactions on the thermodynamics of hydration. The model is able to qualitatively capture the trends seen experimentally, such as the temperature dependence of thermodyamic functions such as the heat capacity and the effect of changing solute size, establishing it as a computationally cheap starting point for more sophisticated 3D models.
Solvation of a simple model hydrophobe is also the subject of a study by Pier Luigi Silvestrelli and colleagues at the University of Padova (L. Rossato et al., J. Phys. Chem. B 116, 4552; 2012 – paper here). They perform first-principles calculations for the hydration of methane, and find that the hydrophobic solute does not (as has been sometimes suggested) lead to a substantial slowing of the dynamics of the few water molecules in the first hydration shell, but rather to a slight (less than twofold) slowing of many water molecules. This slowing is caused by retardation of hydrogen-bond exchange.
More problems for the notion of ions as structure-makers and breakers comes from a study by Nuno Galamba of the University of Lisbon, who uses MD simulations to look at the perturbations of water tetrahedrality in the coordination shells of sodium halides (J. Phys. Chem. B 116, 5242; 2012 – paper here). Galamba points out how confused the current kosmotrope/chaotrope picture already is, for example because the effects of an ion on ‘water structure’ can be quite different in different hydration shells. Galamba concludes that a classification of kosmotropes/chaotropes based on the first hydration shell does not necessarily relate to what happens beyond that, so that the position of an ion in the Hofmeister series does not necessarily relate in a simple or transparent way to its overall effect on the hydrogen-bonded network of water. In terms of the implications for biomolecules, the paper’s final sentence provides, I think, a fair statement of the emerging consensus: “ion−protein interactions are likely to be much more significant than ion-induced long-range water structure perturbations, in agreement with the current view about Hofmeister ion effects on protein stability.”
Not quite the normal “water in biology” fare, but certainly warranting that general description, is a paper by Philippe Marmottant at the University of Grenoble and colleagues on water under tension (O. Vincent et al., Phys. Rev. Lett. 108, 184502; 2012 – paper here). Such water occurs in the xylem of trees, where it is drawn up by transpiration from leaves. I recently saw a very nice presentation on this subject by Adrian Strook at Cornell, who is making studies along similar lines to that reported in this paper. To model the plant system, Marmottant and colleagues use a hydrogel perforated with a regular array of cavities about 50 microns across. The main question they set out to investigate is what drives cavitation when the water pressure becomes increasingly negative – in plants, cavitation threatens to disrupt water transport. The tension here is generated simply by letting water evaporate from the gel. It seems that, when a bubble is nucleated (either spontaneously or stimulated by laser), it grows quickly to a quasi-equilibrium radius and then grows rather slowly larger – a very different process from cavitation in a bulk liquid, where cavitation is typically followed by rapid, energetic and potentially destructive bubble collapse (for example leading to sonoluminescence).
I have seen few more striking examples of the involvement of ‘structured’ hydration water in enzyme action than that supplied by Ursula Rothlisberger at EPFL in Lausanne and colleagues (E. Brunk et al., JACS 134, 8608; 2012 – paper here). They use classical and quantum MD to look at the mechanism of the DNA-repair enzyme MutY, which excises a DNA base damaged by hydroxyl radical oxidation. The first (rate-determining) step of the process involves protonation of the N7 of adenine, which is assisted by a highly organized catalytic cluster of five water molecules, as shown here. The authors suggest that the particular arrangement of hydrophobic and hydrophilic residues around the water cluster act as a ‘water trap’ to ensure that these waters have long residence times.
How hydration influences and perhaps dictates pressure- and cold-induced protein denaturation has been much studied, but is still in debate. Payel Das of IBM Yorktown Heights and Silvina Matysiak of the University of Maryland shed some light on this question with MD simulations of the denaturation of a model 32-mer hydrophobic polymer (J. Phys. Chem. B jp211832c – paper here). They find that folding to the compact state happens via a hairpin-like configuration with a vapour bubble at the elbow, and that high pressure suppresses this process by reducing water fluctuations – observations that seem rather consistent with the current view of dewetting-induced hydrophobic collapse. Cold, meanwhile, leads to enhanced tetrahedral ordering of the hydration shell, which also suppresses the collapse.
Ah, but here’s the thing: cavities – or if you like, vapour bubbles – inside a protein have been generally found to be destabilizing, tending to induce denaturation, as discussed in a Commentary article in PNAS by Brian Matthews of the University of Oregon (PNAS 10.1073/pnas.1204795109 – paper here). This piece is motivated by a paper by Roche et al. (PNAS 109, 6945; 2012 – paper here) looking at the influence of cavities on pressure denaturation, specifically on the pressure-induced unfolding of SNase mutants that have appreciable dry cavities in their interiors. They find that the cavities play a dominant role in the unfolding process via the reduction in protein volume on denaturation.
The coupling of protein and hydration-shell dynamics is the subject of a paper by Jeremy Smith and colleagues at Oak Ridge (L. Hong et al., Phys. Rev. Lett. 108, 238102; 2012 – paper here). They follow the dynamics up to ns timescales in MD simulations and neutron-scattering measurements of lysozyme, and find that the protein dynamics can be decomposed into three components: diffusion within a local potential well, methyl rotations and nonmethyl ‘jumps’ – which I take to be jumps of localized diffusional chain motion from one potential well to another. Hydration seems to increase the probability of these latter jumps, but it also broadens the volume accessible for localized diffusion – in effect making the protein ‘softer’. Moreover, this effect propagates from the solvent-accessible surface deep into the ‘dry’ protein interior, loosening up the entire molecule.
Coupling of hydration dynamics is also the topic of a study by Kevin Kubarych and colleagues at the University of Michigan (J. T. King et al., J. Phys. Chem. B jp300835k – paper here). They use ultrafast IR spectroscopy to probe water dynamics near the surface of two variants of lysozyme. As previous studies have indicated, these dynamics are highly heterogeneous in space, and can vary from bulk-like to highly retarded, the latter being found at extended hydrophobic surfaces and being due to reduced hydrogen-bonding exchange. Using solvent-exchange, they also find that the liberation of this water drives the association of small molecules (and by extension, perhaps other proteins) at the hydrophobic protein surfaces.
Bridging water molecules often play an important catalytic role in receptor-substrate interactions. But not, it seems, in the mechanism of threonyl-tRNA synthetase: James Gauld of the University of Windsor in Canada and colleagues show that, contrary to previous suggestions, a water molecule here seem to serve no useful role, but only disrupts the process (E. A. C. Bushnell et al., J. Phys. Chem. B 116, 5205; 2012 – paper here).
The effect of progressive hydration of a protein from an essentially dry state is studied by Oleg Boyarkin and colleagues at EPFL in Lausanne (N. S. Nagornova et al., Science 336, 320; 2012 – paper here). They form gas-phase clusters of the macrocyclic peptide gramicidin S complexed with various numbers of water molecules, from 1 to 50, and characterize the interactions using vibrational spectroscopy to monitor hydrogen-bonding. The effect of progressive hydration is most pronounced for the first two water molecules, which disrupt intramolecular non-covalent (amine cation to pi) bonds and cause significant elongation of the peptide, bringing it into a conformation close to that of the fully hydrated state.
An interesting preprint on dewetting-induced hydrophobic attraction by Naiyin Yu and Michael Hagan at Brandeis (arxiv:1206.1828 – paper here). The latest view of this picture (see Patel et al., J. Phys. Chem. B 116, 2498 (2012) – Hagan is a coauthor of this paper) posits that proteins that self-assemble via hydrophobic interactions tend to sit close to a dewetting transition, which – if it doesn’t happen spontaneously – might therefore be induced by small perturbations. Yu and Hagan support this idea with simulations of the dimerization of the HIV capsid protein. While the wild-type subunits assemble only by gradual expulsion of water, mutations enacted in silico to replace three hydrophilic residues at the interface with hydrophobic ones can trigger dewetting – and moreover that they do so in a way that reveals the cooperativity of drying and the sensitivity to surface topography. As the authors argue, “Since the CA-C dimerization interface is typical of protein binding surfaces, our results raise the possibility that many proteins sit near a dewetting transition”.
A simple model of the hydration of a hydrophobic particle is presented by Ken Dill of Stony Brook and colleagues in Ljubljana (M. Luksic et al., J. Phys. Chem. B 116, 6177; 2012 – paper here). The model is two-dimensional, with water molecules modelled as ‘Mercedes Benz’ circular particles that engage in trigonal hydrogen bonding – simple enough to be solved almost analytically. The aim here is to probe the effects of hydrogen bonding and van der Waals interactions on the thermodynamics of hydration. The model is able to qualitatively capture the trends seen experimentally, such as the temperature dependence of thermodyamic functions such as the heat capacity and the effect of changing solute size, establishing it as a computationally cheap starting point for more sophisticated 3D models.
Solvation of a simple model hydrophobe is also the subject of a study by Pier Luigi Silvestrelli and colleagues at the University of Padova (L. Rossato et al., J. Phys. Chem. B 116, 4552; 2012 – paper here). They perform first-principles calculations for the hydration of methane, and find that the hydrophobic solute does not (as has been sometimes suggested) lead to a substantial slowing of the dynamics of the few water molecules in the first hydration shell, but rather to a slight (less than twofold) slowing of many water molecules. This slowing is caused by retardation of hydrogen-bond exchange.
More problems for the notion of ions as structure-makers and breakers comes from a study by Nuno Galamba of the University of Lisbon, who uses MD simulations to look at the perturbations of water tetrahedrality in the coordination shells of sodium halides (J. Phys. Chem. B 116, 5242; 2012 – paper here). Galamba points out how confused the current kosmotrope/chaotrope picture already is, for example because the effects of an ion on ‘water structure’ can be quite different in different hydration shells. Galamba concludes that a classification of kosmotropes/chaotropes based on the first hydration shell does not necessarily relate to what happens beyond that, so that the position of an ion in the Hofmeister series does not necessarily relate in a simple or transparent way to its overall effect on the hydrogen-bonded network of water. In terms of the implications for biomolecules, the paper’s final sentence provides, I think, a fair statement of the emerging consensus: “ion−protein interactions are likely to be much more significant than ion-induced long-range water structure perturbations, in agreement with the current view about Hofmeister ion effects on protein stability.”
Not quite the normal “water in biology” fare, but certainly warranting that general description, is a paper by Philippe Marmottant at the University of Grenoble and colleagues on water under tension (O. Vincent et al., Phys. Rev. Lett. 108, 184502; 2012 – paper here). Such water occurs in the xylem of trees, where it is drawn up by transpiration from leaves. I recently saw a very nice presentation on this subject by Adrian Strook at Cornell, who is making studies along similar lines to that reported in this paper. To model the plant system, Marmottant and colleagues use a hydrogel perforated with a regular array of cavities about 50 microns across. The main question they set out to investigate is what drives cavitation when the water pressure becomes increasingly negative – in plants, cavitation threatens to disrupt water transport. The tension here is generated simply by letting water evaporate from the gel. It seems that, when a bubble is nucleated (either spontaneously or stimulated by laser), it grows quickly to a quasi-equilibrium radius and then grows rather slowly larger – a very different process from cavitation in a bulk liquid, where cavitation is typically followed by rapid, energetic and potentially destructive bubble collapse (for example leading to sonoluminescence).
Friday, April 27, 2012
Now with pictures (what took me so long?)
Despite that previous post, I have found a bit of time while on travel, and so here's a catch-up.
Now here’s something very interesting. The ‘dewetting’ theory of protein assembly, according to which hydrophobic surfaces are drawn together at small separations by a cooperative, abrupt drying transition, has been much debated. Simulations have shown that dewetting can happen for flat hydrophobic plates, and also for hydrophobic polymers, but it seems to be rather rare for real proteins, in part because of their chemical heterogeneity: only a few hydrophilic groups on the surfaces are sufficient to suppress the transition, leading instead to gradual molecule-by-molecule expulsion of water. Now Song-Ho Chong and Sihyun Ham of Sookmyung Women’s University in South Korea have looked carefully at one particular protein assembly process: the dimerization of amyloid-beta, a 42-residue peptide linked to Alzheimer’s disease (PNAS doi:10.1073/pnas.1120646109 – paper here). The researchers study the aggregation with MD, and then apply the integral-equation theory of liquids to the simulated conformations to deduce the thermodynamics of solvation. They see no dewetting, but instead two distinct regimes of assembly. At relatively large separations it is the hydrophilic groups that seem to drive the attraction of the monomers, via an enthalpic interaction. Then as the protein surfaces come into contact, there is a switch to an entropically driven process that is water-mediated and involves dehydration of both hydrophobic and hydrophilic groups. I have not before seen anything much like this picture of protein assembly, although it does somewhat bring to mind the water-mediated contacts over long distances (1 nm or so) adduced in protein folding by Papoian et al. (PNAS 101, 3352; 2004).
The dewetting or capillary-evaporation picture of hydrophobic assembly has so far paid scant attention to the rate of water explusion in the hydrophobically confined region. Sumit Sharma and Pablo Debenedetti fill this gap, with some striking conclusions (PNAS 109, 4365; 2012 – paper here). They find that the (predominantly enthalpic) free-energy barrier to evaporation depends sensitively on the separation between the surfaces (assuming here a slit-like geometry), such that a change in separation from 9 to 14 Å results in a rate of evaporation that differs by ten orders of magnitude.
Another view of protein aggregation is offered by Alfonso De Simone at Imperial College in London and colleagues, who have looked at the formation of amyloid structures with non-pathological, functional significance: the hydrophobins that form robust protein coats on fungal spores, making them resistant to wetting (A. De Simone et al., PNAS doi:10.1073/pnas.1118048109 – paper here). What is striking about these proteins is that they are ‘designed’ to remain soluble unless they come into contact with a hydrophobic-hydrophilic interface, such as the air-water interface. The simulations in this study suggest that a section of the peptide chains that is highly flexible and disordered in bulk solution acts to suppress aggregation in that environment. At the air-water interface the proteins have drastically reduced access to his ensemble of conformations.
In contrast to this view, Martin Scholtz of Texas A&M and colleagues say that keeping proteins soluble seems to involve negative surface charge (R. M. Kramer et al., Biophys. J. 102, 1907; 2012 – paper here). They reach this conclusion by studying the effects on solubility of a range of proteins of adding two types of precipitant (that do not denature the proteins they precipitate): ammonium sulphate and polyethylene glycol 8000. They think that the observed correlation between solubility and surface negative charge is probably due to the strong water-binding propensity of glutamate and aspartate groups.
It is in fact the strong hydration promoted by these very groups that has been proposed as the reason for the stability of proteins in halophilic organisms, which have to resist the unfolding and aggregation that high salt concentrations might ordinarily induce. Bertil Halle and colleagues at Lund have probed this idea by looking at the water dynamics hydrating a halophilic protein Kx6E using oxygen-17 NMR (J. Qvist et al., J. Phys. Chem. B 116, 3436; 2012 – paper here). They find that these dynamics are not significantly different from those of the non-halophilic counterpart of this protein, challenging the notion of very tightly bound water molecules in the hydration sphere of halophilic proteins and, for that matter, the suggestion that cell water in extreme halophiles has slower dynamics than that in other cells (M. Tehei et al., PNAS 104, 766; 2007).
In a theoretical study of the hydration of hydrophobic surfaces using density-functional theory, Y. Djikaev and E Ruckenstein at SUNY at Buffalo support this notion that the hydration free energy here is primarily enthalpic (J. Phys. Chem. B 116, 2820; 2012 – paper here). They say that hydration is generally unfavourable at room temperature, and that the hydration free energy increases with increasing temperature, partly because entropic effects become increasingly negligible.
What is the hydrophobic interaction anyway? According to Snyder et al. (PNAS 108, 17889; 2011), we should start thinking in terms of a multiplicity of such effects; the work above seems to offer some endorsement for that view. Classically, the signature of a hydrophobic effect in protein folding has been considered to be a large difference between the heat capacities of the native and unfolded forms. But Robert Baldwin at Stanford, reviewing the history of how hydrophobic effects have been identified and rationalized (PNAS 10.1073/pnas.1203720109; 2012 – paper here), suggests that new definitions of the hydrophobic free energy are needed.
Some months ago, Umeda et al. reported a very beautiful crystal structure of photosystem II at 1.9 Å resolution, including a detailed picture of the hydration sphere (Nature 473, 55; 2011). They argued that several features of the hydration water distribution suggest that it forms a hydrogen-bonded network with specific roles in the catalytic mechanism of water splitting, such as relaying protons or other water molecules to active regions. Brandon Polander and Bridgette Barry at Georgia Tech have now looked at this idea in some detail (PNAS 109, 6112; 2012 – paper here). They focus on the oxygen-evolving complex, containing a Mn-Ca complex in which two water molecules ligate Mn and two Ca. By perturbing this H-bonded network with ammonia (which may substitute for water) and trehalose (which reverses the effect of ammonia), the authors deduce that the network is indeed critical for the photo-oxidation of water leading to oxygen evolution.
More on urea-induced protein denaturation. Yuguang Mu of Nanyang Technological University in Singapore and colleagues use MD simulations to study the salting in/out effects of urea and NaCl on amino acids and on a small amide mimicking a peptide backbone (W. Li et al., J. Phys. Chem. B 116, 1446; 2012 – paper here). They find, in line with experiments, that NaCl induces salting out, and urea salting in. By calculating the thermodynamic driving forces of these effects, they deduce that urea’s effect is caused not by the formation of hydrogen bonds with the peptide side-chain (or here, their mimics) but by an attraction mediated by van der Waals forces. This supports the idea that urea denaturation is mediated by direct interactions with the protein, but challenges the view that these interactions are hydrogen-bonding ones.
Susmita Roy and Biman Bagchi of the Indian Institute of Science in Bangalore present a picture of protein hydration in terms of water molecules in the hydration shell that are separated from the bulk by a free energy barrier against their escape (J. Phys. Chem. B 116, 2958; 2012 – paper here). They present MD simulations of hydration of the chicken villin head piece, which show that the residence time of hydration waters is strongly sensitive to secondary structure. In particular, a small subset of waters in one particular location, constituting about 5-10% of the total hydration shell, have residence times of around 100 ps. They seem to form a cluster that plays a central role in stabilizing the protein conformation by clamping together two of the protein’s three helices. Here then is another example of ‘quasi-bound’ waters becoming what one might consider as an intrinsic (albeit ‘loose’ and exchangeable) part of a protein’s secondary structure.
The effect of molecular crowding on hydration, for too long neglected, seems now to be getting the attention it deserves. The latest study comes from Michael Feig, currently at RIKEN in Kobe, and colleagues (R. Harada et al., JACS 134, 4842; 2012 – paper here). They have looked at how crowding affects water structure in concentrated solutions of a segment of streptococcal protein G by itself and combined with chicken villin head piece. They find that differences in local water density close to the dilute and crowded (>30% protein by volume – a physiological relevant situation) proteins are more pronounced beyond the first hydration shell; in particular, relatively ordered regions in the dilute case are often disrupted by crowding. What’s more, water diffusion is significantly reduced in the crowded case, and the dielectric constant is reduced. That latter change is especially significant, since it should reduce hydrophobic attraction and, by reducing electrostatic shielding, enhance the strength of hydrogen bonds and salt bridges. This in turn might be expected to stabilize secondary structure while destabilizing tertiary structure. These issues must surely be taken seriously in cell biology: how have proteins adapted, as one must assume they have, to withstand these likely perturbations in the strength of the forces that hold them together? What would this imply for protein-ligand binding constants and dissociation rates?
Proteins undergo slow conformational fluctuations, but they also exhibit higher-frequency collective vibrations akin to those seen in disordered matter. What role, if any, does the solvent play in these fast vibrations? Alessandro Paciarone at the Università degli Studi of Perugia and colleagues have investigated this issue by using terahertz spectroscopy to probe the rapid collective vibrations of essentially dry maltose binding protein (A. Paciarone et al., J. Phys. Chem. B 116, 3861; 2012 – paper here). In the dry state these motions tend to be faster, suggesting that as, one might expect, a reduction in hydration brings about an increase in rigidity.
The distribution of many ions in aqueous solution is perturbed at the air-water interface, where the ions may be either selectively adsorbed or depleted. It is not yet clear what drives this segregation, but a paper by Richard Saykally and colleagues at Berkeley sets out to elucidate that (D. E. Otten et al., PNAS 109, 701; 2012 – paper here). They use resonant UV SHG spectroscopy to look at the distribution of thiocyanate ions (classified in the old-style Hofmeister schemes as a typical ‘chaotrope’) at the interface as a function of temperature, in order to measure the thermodynamic variables. They find that the adsorption enthalpy and entropy changes are both negative. The former reflects a balance between hydration and surface energies of the solvent (for example, how much an ion ruptures solvent-solvent hydrogen bonds), whereas the entropy change seems to result from the way adsorbed ions alter capillary-wave fluctuations at the surface. An ion’s Hofmeister effect should therefore reflect a balance of these two, essentially independent factors.
The homogeneity or otherwise of aqueous solutions, particularly those of alcohols and polyols, is a subject of ongoing debate. There seems good reason to suspect that even rather simple alcohols show a significant degree of aggregation. This seems to be true of 2-butoxyethanol, as revealed in simulations by Rini Gupta and G. N. Patey of UBC in Canada (J. Phys. Chem. B 115, 15323; 2011 – paper here). They find that aggregates of the alcohol begin to appear at mole fractions (X) of more than about 0.005, and by X~0.04-0.02 these are micelle-like and rather large, so that large simulation systems (around 32,000 molecules) are needed to accommodate them. The size of the aggregates at these mole fractions – around 4 nm – is big enough to be seen in light-scattering and SANS experiments, as has already been reported.
There’s increasing interest on the structure, dynamics and thermodynamics of biological macromolecules at the air-water interface. Ozge Engin and Mehmet Sayar at Koç University in Turkey have looked at this issue for amphiphilic peptides designed to sit at such interfaces and to self-assemble into ordered systems and nanostructures (J. Phys. Chem. B 116, 2198; 2012 – paper here). Specifically, they look at small peptides designed to fold into beta-hairpins in solution, which could act as models for studying, e.g. amyloid formation. Perhaps unsurprisingly, the segregation of hydrophobic and hydrophilic residues at the water surface promotes hairpin formation above what is observed in bulk solution, and the molecules form well-ordered monolayers with anti-parallel stacking.
There’s a potential synergy here with a paper by David Vaux at Oxford and colleagues on amyloid formation at the air-water interface (L. Jean et al., Biophys. J. 102, 1154; paper here). They find that the interface promotes amyloidogenesis, largely due to a simple concentration effect: the (representative) amyloid peptides they study are surface-active, and so there is enrichment at the air-water boundary (i.e. this does not speak to the issue of whether, say, hydrophobic interactions are altered at the interface). The implications are partly cautionary: such surface effects could be complicating in vitro studies of amyloid formation and drug screening. But as the authors point out, complex interfaces are also present in vivo.
Forgive me if I’ve mentioned this before, but I think somehow I haven’t: there is an excellent summary of David Chandler’s ideas on dewetting and water fluctuations in a preprint with Patrick Varilly prepared for the International School of Physics "Enrico Fermi", Course CLXXVI - "Complex materials in physics and biology" in Varenna, Italy (a very lovely place), which happened back in July 2010. It’s at arxiv/1101.2235 (here), but doesn’t seem to have been published in a proceedings yet.
Now here’s something very interesting. The ‘dewetting’ theory of protein assembly, according to which hydrophobic surfaces are drawn together at small separations by a cooperative, abrupt drying transition, has been much debated. Simulations have shown that dewetting can happen for flat hydrophobic plates, and also for hydrophobic polymers, but it seems to be rather rare for real proteins, in part because of their chemical heterogeneity: only a few hydrophilic groups on the surfaces are sufficient to suppress the transition, leading instead to gradual molecule-by-molecule expulsion of water. Now Song-Ho Chong and Sihyun Ham of Sookmyung Women’s University in South Korea have looked carefully at one particular protein assembly process: the dimerization of amyloid-beta, a 42-residue peptide linked to Alzheimer’s disease (PNAS doi:10.1073/pnas.1120646109 – paper here). The researchers study the aggregation with MD, and then apply the integral-equation theory of liquids to the simulated conformations to deduce the thermodynamics of solvation. They see no dewetting, but instead two distinct regimes of assembly. At relatively large separations it is the hydrophilic groups that seem to drive the attraction of the monomers, via an enthalpic interaction. Then as the protein surfaces come into contact, there is a switch to an entropically driven process that is water-mediated and involves dehydration of both hydrophobic and hydrophilic groups. I have not before seen anything much like this picture of protein assembly, although it does somewhat bring to mind the water-mediated contacts over long distances (1 nm or so) adduced in protein folding by Papoian et al. (PNAS 101, 3352; 2004).
The dewetting or capillary-evaporation picture of hydrophobic assembly has so far paid scant attention to the rate of water explusion in the hydrophobically confined region. Sumit Sharma and Pablo Debenedetti fill this gap, with some striking conclusions (PNAS 109, 4365; 2012 – paper here). They find that the (predominantly enthalpic) free-energy barrier to evaporation depends sensitively on the separation between the surfaces (assuming here a slit-like geometry), such that a change in separation from 9 to 14 Å results in a rate of evaporation that differs by ten orders of magnitude.
Another view of protein aggregation is offered by Alfonso De Simone at Imperial College in London and colleagues, who have looked at the formation of amyloid structures with non-pathological, functional significance: the hydrophobins that form robust protein coats on fungal spores, making them resistant to wetting (A. De Simone et al., PNAS doi:10.1073/pnas.1118048109 – paper here). What is striking about these proteins is that they are ‘designed’ to remain soluble unless they come into contact with a hydrophobic-hydrophilic interface, such as the air-water interface. The simulations in this study suggest that a section of the peptide chains that is highly flexible and disordered in bulk solution acts to suppress aggregation in that environment. At the air-water interface the proteins have drastically reduced access to his ensemble of conformations.
In contrast to this view, Martin Scholtz of Texas A&M and colleagues say that keeping proteins soluble seems to involve negative surface charge (R. M. Kramer et al., Biophys. J. 102, 1907; 2012 – paper here). They reach this conclusion by studying the effects on solubility of a range of proteins of adding two types of precipitant (that do not denature the proteins they precipitate): ammonium sulphate and polyethylene glycol 8000. They think that the observed correlation between solubility and surface negative charge is probably due to the strong water-binding propensity of glutamate and aspartate groups.
It is in fact the strong hydration promoted by these very groups that has been proposed as the reason for the stability of proteins in halophilic organisms, which have to resist the unfolding and aggregation that high salt concentrations might ordinarily induce. Bertil Halle and colleagues at Lund have probed this idea by looking at the water dynamics hydrating a halophilic protein Kx6E using oxygen-17 NMR (J. Qvist et al., J. Phys. Chem. B 116, 3436; 2012 – paper here). They find that these dynamics are not significantly different from those of the non-halophilic counterpart of this protein, challenging the notion of very tightly bound water molecules in the hydration sphere of halophilic proteins and, for that matter, the suggestion that cell water in extreme halophiles has slower dynamics than that in other cells (M. Tehei et al., PNAS 104, 766; 2007).
In a theoretical study of the hydration of hydrophobic surfaces using density-functional theory, Y. Djikaev and E Ruckenstein at SUNY at Buffalo support this notion that the hydration free energy here is primarily enthalpic (J. Phys. Chem. B 116, 2820; 2012 – paper here). They say that hydration is generally unfavourable at room temperature, and that the hydration free energy increases with increasing temperature, partly because entropic effects become increasingly negligible.
What is the hydrophobic interaction anyway? According to Snyder et al. (PNAS 108, 17889; 2011), we should start thinking in terms of a multiplicity of such effects; the work above seems to offer some endorsement for that view. Classically, the signature of a hydrophobic effect in protein folding has been considered to be a large difference between the heat capacities of the native and unfolded forms. But Robert Baldwin at Stanford, reviewing the history of how hydrophobic effects have been identified and rationalized (PNAS 10.1073/pnas.1203720109; 2012 – paper here), suggests that new definitions of the hydrophobic free energy are needed.
Some months ago, Umeda et al. reported a very beautiful crystal structure of photosystem II at 1.9 Å resolution, including a detailed picture of the hydration sphere (Nature 473, 55; 2011). They argued that several features of the hydration water distribution suggest that it forms a hydrogen-bonded network with specific roles in the catalytic mechanism of water splitting, such as relaying protons or other water molecules to active regions. Brandon Polander and Bridgette Barry at Georgia Tech have now looked at this idea in some detail (PNAS 109, 6112; 2012 – paper here). They focus on the oxygen-evolving complex, containing a Mn-Ca complex in which two water molecules ligate Mn and two Ca. By perturbing this H-bonded network with ammonia (which may substitute for water) and trehalose (which reverses the effect of ammonia), the authors deduce that the network is indeed critical for the photo-oxidation of water leading to oxygen evolution.
More on urea-induced protein denaturation. Yuguang Mu of Nanyang Technological University in Singapore and colleagues use MD simulations to study the salting in/out effects of urea and NaCl on amino acids and on a small amide mimicking a peptide backbone (W. Li et al., J. Phys. Chem. B 116, 1446; 2012 – paper here). They find, in line with experiments, that NaCl induces salting out, and urea salting in. By calculating the thermodynamic driving forces of these effects, they deduce that urea’s effect is caused not by the formation of hydrogen bonds with the peptide side-chain (or here, their mimics) but by an attraction mediated by van der Waals forces. This supports the idea that urea denaturation is mediated by direct interactions with the protein, but challenges the view that these interactions are hydrogen-bonding ones.
Susmita Roy and Biman Bagchi of the Indian Institute of Science in Bangalore present a picture of protein hydration in terms of water molecules in the hydration shell that are separated from the bulk by a free energy barrier against their escape (J. Phys. Chem. B 116, 2958; 2012 – paper here). They present MD simulations of hydration of the chicken villin head piece, which show that the residence time of hydration waters is strongly sensitive to secondary structure. In particular, a small subset of waters in one particular location, constituting about 5-10% of the total hydration shell, have residence times of around 100 ps. They seem to form a cluster that plays a central role in stabilizing the protein conformation by clamping together two of the protein’s three helices. Here then is another example of ‘quasi-bound’ waters becoming what one might consider as an intrinsic (albeit ‘loose’ and exchangeable) part of a protein’s secondary structure.
The effect of molecular crowding on hydration, for too long neglected, seems now to be getting the attention it deserves. The latest study comes from Michael Feig, currently at RIKEN in Kobe, and colleagues (R. Harada et al., JACS 134, 4842; 2012 – paper here). They have looked at how crowding affects water structure in concentrated solutions of a segment of streptococcal protein G by itself and combined with chicken villin head piece. They find that differences in local water density close to the dilute and crowded (>30% protein by volume – a physiological relevant situation) proteins are more pronounced beyond the first hydration shell; in particular, relatively ordered regions in the dilute case are often disrupted by crowding. What’s more, water diffusion is significantly reduced in the crowded case, and the dielectric constant is reduced. That latter change is especially significant, since it should reduce hydrophobic attraction and, by reducing electrostatic shielding, enhance the strength of hydrogen bonds and salt bridges. This in turn might be expected to stabilize secondary structure while destabilizing tertiary structure. These issues must surely be taken seriously in cell biology: how have proteins adapted, as one must assume they have, to withstand these likely perturbations in the strength of the forces that hold them together? What would this imply for protein-ligand binding constants and dissociation rates?
Proteins undergo slow conformational fluctuations, but they also exhibit higher-frequency collective vibrations akin to those seen in disordered matter. What role, if any, does the solvent play in these fast vibrations? Alessandro Paciarone at the Università degli Studi of Perugia and colleagues have investigated this issue by using terahertz spectroscopy to probe the rapid collective vibrations of essentially dry maltose binding protein (A. Paciarone et al., J. Phys. Chem. B 116, 3861; 2012 – paper here). In the dry state these motions tend to be faster, suggesting that as, one might expect, a reduction in hydration brings about an increase in rigidity.
The distribution of many ions in aqueous solution is perturbed at the air-water interface, where the ions may be either selectively adsorbed or depleted. It is not yet clear what drives this segregation, but a paper by Richard Saykally and colleagues at Berkeley sets out to elucidate that (D. E. Otten et al., PNAS 109, 701; 2012 – paper here). They use resonant UV SHG spectroscopy to look at the distribution of thiocyanate ions (classified in the old-style Hofmeister schemes as a typical ‘chaotrope’) at the interface as a function of temperature, in order to measure the thermodynamic variables. They find that the adsorption enthalpy and entropy changes are both negative. The former reflects a balance between hydration and surface energies of the solvent (for example, how much an ion ruptures solvent-solvent hydrogen bonds), whereas the entropy change seems to result from the way adsorbed ions alter capillary-wave fluctuations at the surface. An ion’s Hofmeister effect should therefore reflect a balance of these two, essentially independent factors.
The homogeneity or otherwise of aqueous solutions, particularly those of alcohols and polyols, is a subject of ongoing debate. There seems good reason to suspect that even rather simple alcohols show a significant degree of aggregation. This seems to be true of 2-butoxyethanol, as revealed in simulations by Rini Gupta and G. N. Patey of UBC in Canada (J. Phys. Chem. B 115, 15323; 2011 – paper here). They find that aggregates of the alcohol begin to appear at mole fractions (X) of more than about 0.005, and by X~0.04-0.02 these are micelle-like and rather large, so that large simulation systems (around 32,000 molecules) are needed to accommodate them. The size of the aggregates at these mole fractions – around 4 nm – is big enough to be seen in light-scattering and SANS experiments, as has already been reported.
There’s increasing interest on the structure, dynamics and thermodynamics of biological macromolecules at the air-water interface. Ozge Engin and Mehmet Sayar at Koç University in Turkey have looked at this issue for amphiphilic peptides designed to sit at such interfaces and to self-assemble into ordered systems and nanostructures (J. Phys. Chem. B 116, 2198; 2012 – paper here). Specifically, they look at small peptides designed to fold into beta-hairpins in solution, which could act as models for studying, e.g. amyloid formation. Perhaps unsurprisingly, the segregation of hydrophobic and hydrophilic residues at the water surface promotes hairpin formation above what is observed in bulk solution, and the molecules form well-ordered monolayers with anti-parallel stacking.
There’s a potential synergy here with a paper by David Vaux at Oxford and colleagues on amyloid formation at the air-water interface (L. Jean et al., Biophys. J. 102, 1154; paper here). They find that the interface promotes amyloidogenesis, largely due to a simple concentration effect: the (representative) amyloid peptides they study are surface-active, and so there is enrichment at the air-water boundary (i.e. this does not speak to the issue of whether, say, hydrophobic interactions are altered at the interface). The implications are partly cautionary: such surface effects could be complicating in vitro studies of amyloid formation and drug screening. But as the authors point out, complex interfaces are also present in vivo.
Forgive me if I’ve mentioned this before, but I think somehow I haven’t: there is an excellent summary of David Chandler’s ideas on dewetting and water fluctuations in a preprint with Patrick Varilly prepared for the International School of Physics "Enrico Fermi", Course CLXXVI - "Complex materials in physics and biology" in Varenna, Italy (a very lovely place), which happened back in July 2010. It’s at arxiv/1101.2235 (here), but doesn’t seem to have been published in a proceedings yet.
Friday, April 13, 2012
Small and often
My new resolution is to try to post more often and in smaller chunks, not least to avoid an impression of this site being moribund. With that in mind, I acknowledge that there is a fair bit of old stuff to catch up on which is not yet covered here. I also hope, when I have a moment, to find a way of posting that will make this blog accessible in China, which it is not at present because it seems the whole hosting network is blocked due to Google-related wrangles.
Water in protein hydration shells has retarded dynamics, for example in terms of reorientation. But how much and why? Reports vary, from slowing by a factor of a few to several orders of magnitude. Damien Laage and colleagues at ENS in Paris have tried to clarify the situation with simulations of lysozyme (F. Sterpone et al., JACS 134, 4116; 2012 – paper here). They find that most (80%) of the hydration water is slowed by a factor of just 2-3, and that the dynamics seem to be dominated by the same kind of activated jumps between H-bond acceptors as in the bulk. This slowdown seems to be due to an excluded-volume effect from the proximity of the protein surface, which reduces the number of transition-state configurations for reorienting jumps. The remaining water may be slowed to a greater degree, apparently due to water bound within clefts and pockets on the protein surface, where generally it is bound to H-bond acceptors.
Ben Corry and Michael Thomas at the University of Western Australia say that water plays a role in the selectivity of voltage-gated sodium channels (JACS 134, 1840; 2012 – paper here). Simulations based on a recent crystal structure show that unlike sodium, potassium ions can’t fit between a plane of glutamate residues with water molecules bridging the ion and the carboxylate groups – so these latter ions are excluded even though in principle they could pass through the pore with their complete hydration shell. This suggests that there are more subtle structural factors at work than (as has been suggested previously) simply the free-energy penalty of ion dehydration.
The hydrophobic effect and its role in the assembly of hydrophobic particles has generally been considered from the perspective of an equilibrium process, with no account of hydrodynamic factors. Bruce Berne and his coworkers at Columbia now seek to rectify this (J. A. Morrone et al., J. Phys. Chem. B 116, 378; 2012 – paper here). They simulate the interactions of two fullerenes in water, taking into account how molecular-scale hydrodynamics affects solvent density fluctuations and drying transitions. Perhaps unsurprisingly, a continuum picture breaks down at the smallest length scales : for example, the friction coefficient deviates from the continuum prediction at small particle separations, and can become non-monotonic due to layering. In general, these hydrodynamic effects can significantly reduce the diffusion-controlled rate constant for hydrophobic assembly. As the authors say, how such effects would become manifest in the crowded environment of the cell is another matter.
When is a protein unfolded? It’s not such an easy question as one might suppose: Sunilkumar Puthenpurackal Narayanan and colleagues in Japan say (Biophys. J. 102, L08 – paper here) that Catherine Royer and colleagues have recently found that staphylococcal nuclease can show a proton NMR signal at high pressures indicative of complete folding while Trp fluorescence data suggest significant unfolding. Narayanan et al. see something comparable for a subdomain of the transcription factor c-Myb R2 at high pressure and low temperature. This, they say, seems to be explicable on the basis that the protein remains folded but extensively hydrated, owing to water filling of a large internal cavity. This adds to the ongoing debate about the mechanism of pressure-induced denaturation, which some say is caused by the intrusion of water. More on this in a later post.
I wish I had a better grasp of a paper by Vladimir Sirotkin and Aigul Khadiullina of the Kazan Federal University in Russia on excess partial enthalpies of water and proteins (J. Chem. Phys. B 115, 15110; 2011 – paper here). But the key point seems to be that the progression from more or less dehydrated to fully hydrated states of several different proteins follow the same trajectory, at least in thermodynamic terms. The excess partial enthalpy is initially dominated by water, but then up to a weight fraction of 0.06 both protein and water contribute significantly. At this point the charged groups on the protein are hydrated and the proteins become flexible. And by a weight fraction of 0.5, hydration is complete and further changes are due only to contributions from the proteins. This seems loosely to be in accord with notions of a roughly universal ‘critical coverage’ for a protein hydration shell.
Water in protein hydration shells has retarded dynamics, for example in terms of reorientation. But how much and why? Reports vary, from slowing by a factor of a few to several orders of magnitude. Damien Laage and colleagues at ENS in Paris have tried to clarify the situation with simulations of lysozyme (F. Sterpone et al., JACS 134, 4116; 2012 – paper here). They find that most (80%) of the hydration water is slowed by a factor of just 2-3, and that the dynamics seem to be dominated by the same kind of activated jumps between H-bond acceptors as in the bulk. This slowdown seems to be due to an excluded-volume effect from the proximity of the protein surface, which reduces the number of transition-state configurations for reorienting jumps. The remaining water may be slowed to a greater degree, apparently due to water bound within clefts and pockets on the protein surface, where generally it is bound to H-bond acceptors.
Ben Corry and Michael Thomas at the University of Western Australia say that water plays a role in the selectivity of voltage-gated sodium channels (JACS 134, 1840; 2012 – paper here). Simulations based on a recent crystal structure show that unlike sodium, potassium ions can’t fit between a plane of glutamate residues with water molecules bridging the ion and the carboxylate groups – so these latter ions are excluded even though in principle they could pass through the pore with their complete hydration shell. This suggests that there are more subtle structural factors at work than (as has been suggested previously) simply the free-energy penalty of ion dehydration.
The hydrophobic effect and its role in the assembly of hydrophobic particles has generally been considered from the perspective of an equilibrium process, with no account of hydrodynamic factors. Bruce Berne and his coworkers at Columbia now seek to rectify this (J. A. Morrone et al., J. Phys. Chem. B 116, 378; 2012 – paper here). They simulate the interactions of two fullerenes in water, taking into account how molecular-scale hydrodynamics affects solvent density fluctuations and drying transitions. Perhaps unsurprisingly, a continuum picture breaks down at the smallest length scales : for example, the friction coefficient deviates from the continuum prediction at small particle separations, and can become non-monotonic due to layering. In general, these hydrodynamic effects can significantly reduce the diffusion-controlled rate constant for hydrophobic assembly. As the authors say, how such effects would become manifest in the crowded environment of the cell is another matter.
When is a protein unfolded? It’s not such an easy question as one might suppose: Sunilkumar Puthenpurackal Narayanan and colleagues in Japan say (Biophys. J. 102, L08 – paper here) that Catherine Royer and colleagues have recently found that staphylococcal nuclease can show a proton NMR signal at high pressures indicative of complete folding while Trp fluorescence data suggest significant unfolding. Narayanan et al. see something comparable for a subdomain of the transcription factor c-Myb R2 at high pressure and low temperature. This, they say, seems to be explicable on the basis that the protein remains folded but extensively hydrated, owing to water filling of a large internal cavity. This adds to the ongoing debate about the mechanism of pressure-induced denaturation, which some say is caused by the intrusion of water. More on this in a later post.
I wish I had a better grasp of a paper by Vladimir Sirotkin and Aigul Khadiullina of the Kazan Federal University in Russia on excess partial enthalpies of water and proteins (J. Chem. Phys. B 115, 15110; 2011 – paper here). But the key point seems to be that the progression from more or less dehydrated to fully hydrated states of several different proteins follow the same trajectory, at least in thermodynamic terms. The excess partial enthalpy is initially dominated by water, but then up to a weight fraction of 0.06 both protein and water contribute significantly. At this point the charged groups on the protein are hydrated and the proteins become flexible. And by a weight fraction of 0.5, hydration is complete and further changes are due only to contributions from the proteins. This seems loosely to be in accord with notions of a roughly universal ‘critical coverage’ for a protein hydration shell.
Thursday, January 19, 2012
More dynamical transitions?
Francesco Mallamace at MIT/Messina and colleagues have used proton NMR to follow the rearrangements of water during the thermal (heat and cold) denaturation of lysozyme (F. Mallamace et al., J. Phys. Chem. B 115, 14280; 2011 – paper here). Since the chemical shift is considered to probe hydrogen-bonding interactions in the water network, tracking it as the temperature changes take the protein from the folded to the denatured states reveal some aspects of how changes in protein structure are mirrored by those of the hydration water. The researchers conclude that water plays an active role in the process, and that as denaturation proceeds, the average number of H-bonds with which each water molecule is involved changes correspondingly.
How glycerol acts as a cryoprotectant is the subject of a study by J. Towey and L. Dougan at Leeds (J. Phys. Chem. B jp2093862 - paper here). They use neutron scattering to investigate whether, as one hypothesis has it, dissolved glycerol perturbs water structure to modify the hydrogen bonding ability and suppress ice formation. The solution turns out to be well mixed, with many glycerol monomers, but there is no discernible perturbation of the first coordination shell of water. The second shell, however, is perturbed in a manner similar to that caused by elevated pressure. Quite what this means for “the ability of water molecules to form ice” isn’t clear (indeed, I’m not even too sure what that expression means – displacement of the phase boundary?), but Towey and Dougan conclude that any explanation will need to focus not simply on local perturbations (or changes to water’s ability to form hydrogen bonds) but on changes to the extended hydrogen-bonded network.
More on the mechanisms of osmolytes: Dave Thirumalai and colleagues at Maryland have studied the stabilization of compact peptide conformations by trimethylamine N-oxide (TMAO) (S. S. Cho et al., J. Phys. Chem. B 115, 13401; 2011 – paper here). They attribute it to direct interactions between TMAO and the protein surface, which exclude solvent there. This is then a kind of excluded-volume effect analogous to the stabilization of proteins by molecular crowding (in which there is entropic destabilization of the unfolded state) – making TMAO a ‘nanocrowding’ particle.
In a related vein, M. Paulaitis at Ohio State and colleagues describe an integral-equation approach to deduce preferential interactions between cosolvents, which they say can be used to deduce preferential interactions of cosolvents such as osmolytes, naturants and cryoprotectants locally on the surface of proteins (M. H. Priya et al., J. Chem. Phys. B 115, 13633; 2011 – paper here).
Personally, I find it hard to think about hydration in crowded environments, in which marcomolecules might disturb one another’s hydration shells and sometimes temporarily associate with one another in non-specific ways. Sergio Hassan and Peter Steinbach at NIH have tried to provide a context from framing this question (J. Phys. Chem. B 115, 14668; 2011 – paper here). One issue is how incomplete and anisotropic hydration might create electrostatic effects. Another is how solvation forces due to structured hydration shells (layering, for example) manifest themselves on hydrogen-bonding at solute-water interfaces. Using a continuum solvent model, they say that the electrostatic effects of solvent exclusion can have a strong impact on protein-protein binding. But I think it fair to say that at this point the paper is largely presenting the methodology for investigating the problem, rather than reaching general conclusions about how these aspects of crowding affect the molecular biology.
Confinement will, of course, do other things to water itself. Ivan Brovchenko and Alla Oleinikova have predicted that water in slit-like pores just 2.4 nm wide might undergo the liquid-liquid transition predicted in the metastable bulk at low temperature and high pressure (J. Chem. Phys. 126, 214701; 2007). Limei Xu and Valeria Molinero at Utah have now examined that idea in simulations using their mW model of water held within 1.5-nm diameter cylindrical pores (J. Phys. Chem. B 115, 14210; 2011 – paper here). This system is comparable to the pores of MCM-41 nanoporous silica, as used in recent experiments on confined water (e.g. L. Liu et al., Phys. Rev. Lett. 95, 117802 (2005)). They find no evidence for a first-order liquid-liquid transition, but note that smearing of discontinuous transitions is well known in pores (although not in fact inevitable), and therefore that this doesn’t rule out the existence of such a transition in the bulk. For their simulations of the bulk phase, they do see a possible signature of a L-L critical point – a locus of maximum compressibility – but can’t study this in detail because fast crystallization makes it impossible to equilibrate a metastable water phase in this region.
How do proteins remain dynamic while remaining soluble and resistant to aggregation? Fabrizio Chiti at the University of Florence, Chris Dobson at Cambridge, and their colleagues, have sought to answer this by combining NMR relaxation data, H/D exchange experiments and MD simulations (A. De Simone et al., PNAS 108, 21057; 2011 – paper here). They use the fruitfly acylphosphatase as their model system, and find that the wild-type protein has free-energy barriers that limit access to aggregation-prone conformations except under aggrtegation-prone conditions (addition of small amounts of trifluoroethanol). They sum up the situation nicely: “The sensitivity of the energy surfaces of proteins to minor perturbations supports the view that there is a delicate balance between functionality, stability, and solubility, which is encapsulated by the concept of ‘life on the edge’”.
Hydrogen bonds hydrating hydrophobic regions of a protein or peptide seem to have a greater strength than those in bulk water. It’s been suggested that this might be not so much because the H-bonds are genuinely strengthened but because the orientational preferences of H-bonds in such a situation result in a depletion of weaker, strained H-bonds, i.e. a change in the population (Zichi & Rossky, J. Chem. Phys. 83, 797 (1985)). Peter Rossky and colleagues have now explored this idea further using MD simulations of a 16-residue peptide (J. Phys. Chem. B 115, 14859; 2011 – paper here). They find support for the idea, namely, water is depleted of near neighbours around apolar groups and so samples lower-coordination configurations that are undistorted and unstrained. In other words, the phenomenon is primarly a kind of packing effect.
A new angle on Hofmeister effects is offered by Huib Bakker at FOM Institute for Atomic and Molecular Physics in Amsterdam, who have looked at the orientational dynamics of water around various ions (K. J. Tielrooij et al., J. Chem. Phys. B 115, 12638; 2011 – paper here). When the salt consists of a strongly hydrated ion and a weakly hydrated counterion, the water molecules hydrating the former have impeded orientational dynamics, making it strongly anisotropic. In that case, they say that hydration is ‘semi-rigid’ in the first hydration shell: affected along one vector but not along others. If both ions are strongly hydrated, such perturbations of water dynamics extend well beyond the first hydration shell.
And while we’re there: Daryl Eggers and colleagues at San José State University have taken a thermodynamic line of attack on Hofmeister by determining the molar water volumes in various concentrated electrolyte solutions (A. Y. Payumo et al., J. Phys. Chem. B 115, 14784; 2011 – paper here). They find that the solutions are highly nonideal, presumably because of strong competition under these conditions for hydration water. Moreover, the solubility of the small amide diketopiperazine follows the Hofmeister series for all the anions and cations studied, and the authors explain this on the basis that Hofmeister effects are governed by changes in the average free energy of the bulk aqueous phase – that is, if Hofmeister effects are a bulk phenomenon of water.
The tale of the low-temperature dynamical crossover for hydrated proteins and their hydration shells continues to get more complicated. Using dielectric spectroscopy and MC simulations, Gene Stanley, Giancarlo Franzese and their colleagues now report evidence of two such crossovers for the hydration water of lysozyme: one at about 252 K, the other around 181 K (M. G. Mazza et al., PNAS 108, 19873; 2011 – paper here). Marie-Claire Bellissent-Funel and her colleagues have previously seen something similar – two transitions at 220 and 150 K (J.-M. Zanotti et al., PCCP 10, 4865; 2008). Stanley et al. now ascribe the first of these to maximal fluctuations in the making and breaking of hydrogen bonds, and the second to maximal fluctuations in cooperative reordering of the H-bonded network.
Meanwhile, Sol Gruner and colleagues at Cornell report evidence for another protein dynamical transition right down at 110 K, which they say correlates with the transition of the hydration water from a high- to a low-density amorphous state (C. U. Kim et al., PNAS 108, 20897; 2011 – paper here).
Wilfred van Gunsterden at ETH and colleagues show how solvation free energies, as well as the free energies of protein-ligand binding and protein conformational dynamics, can be calculated using a new software package called GROMOS, which van Gunsterden and colleagues have introduced in a paper in press with Comput. Phys. Commun. (S. Riniker et al., J. Phys. Chem. B 115, 13570; 2011 – paper here).
Alan Soper has an intriguing paper in J. Phys. Chem. B (115, 14014; 2011 – paper here) in which he presents a new mixture model of water. This isn’t exactly a two-state model – the two forms are intimately mixed – but it postulates two populations of water molecules, each of which can form hydrogen bonds only with molecules of the other type and not with those of their own type. This is not, as far as I can see, intended as a literal representation of some molecular-scale distinction – both types of water molecule have identical structure – but is imposed as a device for introducing a three-body term into the interactions. The results show good agreement with structural studies using neutron and X-ray scattering, and give rise to a situation where water molecules are H-bonded to some of their neighbours but not others. This, Alan suggests, is perhaps why mixture models of water have been so enduring: not because there really are two distinct populations but because – if I’m understanding this correctly – the three-body terms have the effect of making it appear that way.
Michele Parrinello and colleagues at ETH have investigated the recombination of hydronium and hydroxide ions in water using ab initio MD simulations (A. Hassanali et al., PNAS 108, 20410; 2011 – paper here). They find that the mechanism is rather different from what has traditionally been assumed in terms of a Grotthuss mechanism. The researchers say that the Grotthuss mechanism serves to bring the hydronium and hydroxide to a distance of around 6 Å, when they are bridged by two water molecules as a ‘water wire’. But then there is a collective compression of this water wire that results in a concerted motion of three protons (rather than a series of distinct one-proton hops), converting both ions into water molecules.
How glycerol acts as a cryoprotectant is the subject of a study by J. Towey and L. Dougan at Leeds (J. Phys. Chem. B jp2093862 - paper here). They use neutron scattering to investigate whether, as one hypothesis has it, dissolved glycerol perturbs water structure to modify the hydrogen bonding ability and suppress ice formation. The solution turns out to be well mixed, with many glycerol monomers, but there is no discernible perturbation of the first coordination shell of water. The second shell, however, is perturbed in a manner similar to that caused by elevated pressure. Quite what this means for “the ability of water molecules to form ice” isn’t clear (indeed, I’m not even too sure what that expression means – displacement of the phase boundary?), but Towey and Dougan conclude that any explanation will need to focus not simply on local perturbations (or changes to water’s ability to form hydrogen bonds) but on changes to the extended hydrogen-bonded network.
More on the mechanisms of osmolytes: Dave Thirumalai and colleagues at Maryland have studied the stabilization of compact peptide conformations by trimethylamine N-oxide (TMAO) (S. S. Cho et al., J. Phys. Chem. B 115, 13401; 2011 – paper here). They attribute it to direct interactions between TMAO and the protein surface, which exclude solvent there. This is then a kind of excluded-volume effect analogous to the stabilization of proteins by molecular crowding (in which there is entropic destabilization of the unfolded state) – making TMAO a ‘nanocrowding’ particle.
In a related vein, M. Paulaitis at Ohio State and colleagues describe an integral-equation approach to deduce preferential interactions between cosolvents, which they say can be used to deduce preferential interactions of cosolvents such as osmolytes, naturants and cryoprotectants locally on the surface of proteins (M. H. Priya et al., J. Chem. Phys. B 115, 13633; 2011 – paper here).
Personally, I find it hard to think about hydration in crowded environments, in which marcomolecules might disturb one another’s hydration shells and sometimes temporarily associate with one another in non-specific ways. Sergio Hassan and Peter Steinbach at NIH have tried to provide a context from framing this question (J. Phys. Chem. B 115, 14668; 2011 – paper here). One issue is how incomplete and anisotropic hydration might create electrostatic effects. Another is how solvation forces due to structured hydration shells (layering, for example) manifest themselves on hydrogen-bonding at solute-water interfaces. Using a continuum solvent model, they say that the electrostatic effects of solvent exclusion can have a strong impact on protein-protein binding. But I think it fair to say that at this point the paper is largely presenting the methodology for investigating the problem, rather than reaching general conclusions about how these aspects of crowding affect the molecular biology.
Confinement will, of course, do other things to water itself. Ivan Brovchenko and Alla Oleinikova have predicted that water in slit-like pores just 2.4 nm wide might undergo the liquid-liquid transition predicted in the metastable bulk at low temperature and high pressure (J. Chem. Phys. 126, 214701; 2007). Limei Xu and Valeria Molinero at Utah have now examined that idea in simulations using their mW model of water held within 1.5-nm diameter cylindrical pores (J. Phys. Chem. B 115, 14210; 2011 – paper here). This system is comparable to the pores of MCM-41 nanoporous silica, as used in recent experiments on confined water (e.g. L. Liu et al., Phys. Rev. Lett. 95, 117802 (2005)). They find no evidence for a first-order liquid-liquid transition, but note that smearing of discontinuous transitions is well known in pores (although not in fact inevitable), and therefore that this doesn’t rule out the existence of such a transition in the bulk. For their simulations of the bulk phase, they do see a possible signature of a L-L critical point – a locus of maximum compressibility – but can’t study this in detail because fast crystallization makes it impossible to equilibrate a metastable water phase in this region.
How do proteins remain dynamic while remaining soluble and resistant to aggregation? Fabrizio Chiti at the University of Florence, Chris Dobson at Cambridge, and their colleagues, have sought to answer this by combining NMR relaxation data, H/D exchange experiments and MD simulations (A. De Simone et al., PNAS 108, 21057; 2011 – paper here). They use the fruitfly acylphosphatase as their model system, and find that the wild-type protein has free-energy barriers that limit access to aggregation-prone conformations except under aggrtegation-prone conditions (addition of small amounts of trifluoroethanol). They sum up the situation nicely: “The sensitivity of the energy surfaces of proteins to minor perturbations supports the view that there is a delicate balance between functionality, stability, and solubility, which is encapsulated by the concept of ‘life on the edge’”.
Hydrogen bonds hydrating hydrophobic regions of a protein or peptide seem to have a greater strength than those in bulk water. It’s been suggested that this might be not so much because the H-bonds are genuinely strengthened but because the orientational preferences of H-bonds in such a situation result in a depletion of weaker, strained H-bonds, i.e. a change in the population (Zichi & Rossky, J. Chem. Phys. 83, 797 (1985)). Peter Rossky and colleagues have now explored this idea further using MD simulations of a 16-residue peptide (J. Phys. Chem. B 115, 14859; 2011 – paper here). They find support for the idea, namely, water is depleted of near neighbours around apolar groups and so samples lower-coordination configurations that are undistorted and unstrained. In other words, the phenomenon is primarly a kind of packing effect.
A new angle on Hofmeister effects is offered by Huib Bakker at FOM Institute for Atomic and Molecular Physics in Amsterdam, who have looked at the orientational dynamics of water around various ions (K. J. Tielrooij et al., J. Chem. Phys. B 115, 12638; 2011 – paper here). When the salt consists of a strongly hydrated ion and a weakly hydrated counterion, the water molecules hydrating the former have impeded orientational dynamics, making it strongly anisotropic. In that case, they say that hydration is ‘semi-rigid’ in the first hydration shell: affected along one vector but not along others. If both ions are strongly hydrated, such perturbations of water dynamics extend well beyond the first hydration shell.
And while we’re there: Daryl Eggers and colleagues at San José State University have taken a thermodynamic line of attack on Hofmeister by determining the molar water volumes in various concentrated electrolyte solutions (A. Y. Payumo et al., J. Phys. Chem. B 115, 14784; 2011 – paper here). They find that the solutions are highly nonideal, presumably because of strong competition under these conditions for hydration water. Moreover, the solubility of the small amide diketopiperazine follows the Hofmeister series for all the anions and cations studied, and the authors explain this on the basis that Hofmeister effects are governed by changes in the average free energy of the bulk aqueous phase – that is, if Hofmeister effects are a bulk phenomenon of water.
The tale of the low-temperature dynamical crossover for hydrated proteins and their hydration shells continues to get more complicated. Using dielectric spectroscopy and MC simulations, Gene Stanley, Giancarlo Franzese and their colleagues now report evidence of two such crossovers for the hydration water of lysozyme: one at about 252 K, the other around 181 K (M. G. Mazza et al., PNAS 108, 19873; 2011 – paper here). Marie-Claire Bellissent-Funel and her colleagues have previously seen something similar – two transitions at 220 and 150 K (J.-M. Zanotti et al., PCCP 10, 4865; 2008). Stanley et al. now ascribe the first of these to maximal fluctuations in the making and breaking of hydrogen bonds, and the second to maximal fluctuations in cooperative reordering of the H-bonded network.
Meanwhile, Sol Gruner and colleagues at Cornell report evidence for another protein dynamical transition right down at 110 K, which they say correlates with the transition of the hydration water from a high- to a low-density amorphous state (C. U. Kim et al., PNAS 108, 20897; 2011 – paper here).
Wilfred van Gunsterden at ETH and colleagues show how solvation free energies, as well as the free energies of protein-ligand binding and protein conformational dynamics, can be calculated using a new software package called GROMOS, which van Gunsterden and colleagues have introduced in a paper in press with Comput. Phys. Commun. (S. Riniker et al., J. Phys. Chem. B 115, 13570; 2011 – paper here).
Alan Soper has an intriguing paper in J. Phys. Chem. B (115, 14014; 2011 – paper here) in which he presents a new mixture model of water. This isn’t exactly a two-state model – the two forms are intimately mixed – but it postulates two populations of water molecules, each of which can form hydrogen bonds only with molecules of the other type and not with those of their own type. This is not, as far as I can see, intended as a literal representation of some molecular-scale distinction – both types of water molecule have identical structure – but is imposed as a device for introducing a three-body term into the interactions. The results show good agreement with structural studies using neutron and X-ray scattering, and give rise to a situation where water molecules are H-bonded to some of their neighbours but not others. This, Alan suggests, is perhaps why mixture models of water have been so enduring: not because there really are two distinct populations but because – if I’m understanding this correctly – the three-body terms have the effect of making it appear that way.
Michele Parrinello and colleagues at ETH have investigated the recombination of hydronium and hydroxide ions in water using ab initio MD simulations (A. Hassanali et al., PNAS 108, 20410; 2011 – paper here). They find that the mechanism is rather different from what has traditionally been assumed in terms of a Grotthuss mechanism. The researchers say that the Grotthuss mechanism serves to bring the hydronium and hydroxide to a distance of around 6 Å, when they are bridged by two water molecules as a ‘water wire’. But then there is a collective compression of this water wire that results in a concerted motion of three protons (rather than a series of distinct one-proton hops), converting both ions into water molecules.
Tuesday, January 10, 2012
Welcome to 2012
Lots to catch up on here, and while I’m not going to do that exhaustively now, here is an update to let you know that this blog will still be active in 2012.
I’ve recently written a News & Views article for Nature (478, 467; 2011 – here) about, among other things, the recent paper by George Whitesides’ group (PNAS 108, 17889; 2011 – paper here) on the hydrophobic effect in ligand binding – which, as discussed in the previous post, suggests that there is not any single ‘hydrophobic effect’ operating here, but a delicate and case-specific balance of enthalpic and entropic effects. They noted that in the example they studied, the ‘hydrophobic’ aspect of binding was driven largely by the enthalpic effect of displacing/rearranging water around nonpolar contacts. That notion is supported by a paper by Stephen Martin and colleages at the University of Texas at Austin, who find something rather similar for small peptide binding by the SH2 domain of the growth receptor binding protein Grb2 (J. M. Myslinski et al., JACS 133, 18518; 2011 – paper here). They say that increases in the nonpolar contact area don’t necessarily lead to entropic gains due to release of water, but have a primarily enthalpic influence on binding affinity.
How quickly drugs bind to their target molecules can have important pharmacological implications, but these kinetics are generally poorly understood, and thus to design rationally. Xavier Barril from the University of Barcelona and colleagues show using MD simulations that slow kinetics are often a consequence of the presence of buried polar atoms which form hydrogen bonds that are shielded from water, because of the slowness of dehydration/rehydration (P. Schmidtke et al., JACS ja207494u – paper here). In other words, the pace of events in binding can be set by the degree of water accessibility. They show that this effect can be predicted from structural data, and can thus potentially be accessible to design.
Knowing the hydration structure of proteins is important for small-/wide-angle X-ray scattering (SWAXS) studies of proteins not so much for its own sake but because the contribution of the solvent to the scattering must be subtracted in order to extract information about the protein secondary structure. It’s easy enough to extract the contribution of bulk water, but correcting for the scattering of the hydration shell is complicated. Tobin Sosnick and coworkers at the University of Chicago now show two ways to do this (J. J. Virtanen et al., Biophys. J. 101, 2061-2069; 2011 – paper here). One is to deduce the solvation structure by full MD simulations, which they say gives results that match the SWAXS data closely. But they have also developed a much more computationally less intense solvation model called HyPred, which gives a scattering profile that agrees well both with MD and with experiment.
Bernhardt Trout and his coworkers at MIT present an illustration of just how complex the interactons of proteins and ions can be (D. Shukla et al., JACS ja205215t – paper here). Complex ions such as guanidinium create a particularly intricate picture. Gdm+ can destabilize proteins via the formation of hydrogen bonds and electrostatic interactions, but when paired with an anion that is a hydrogen-bonding acceptor it can form clusters with the ions, which suppresses the effect. Molecules (such as arginine) with multiple Gdm+ groups are sometimes used to suppress protein aggregation, and can do so without compromising protein stability. Trout and colleagues investigate the effect of arginine oligomers (n=1-4) on protein aggregation and conformational stability for two different anions, chloride and sulphate. While monomeric arginine chloride is used as an aggregation suppressor, the n-mers only inhibit aggregation at low concentration – they actually accelerate it at moderate to high concentration. Meanwhile, the sulphates inhibit aggregation at all concentrations. And while the chlorides reduce protein stability, the sulphates enhance it. The researchers explain all this in terms of the balance between ion-ion and ion-protein interactions.
All this mirrors an increasing tendency to consider Hofmeister effects of ions on proteins in terms of direct interactions between the two species, rather than as indirect consequences of changes in hydration. Elena Algaer and Nico van der Vegt at the TU Darmstadt provide some support for this notion with a study of the salting-in and –out of small model amides by various sodium salts (J. Phys. Chem. B jp208583w – paper here). They say, for example, that the salting-in if NiPAM by NaI is mediated by interactions of iodide with the nonpolar groups. Such interactions also explain why, of all the salts studied, the iodide alone fails to induce hydrophobic collapse of polyNiPAM.
How does water permeate cell membranes? Its passage through the water-regulating membrane protein aquaporin is fairly well studied, but little is known about other water transporters. The bacterial sodium-galactose transporter vSGLT and its human homologue the sodium-glucose cotransporter hSGLT1 both have the potential to let water through. Jean-Yves Lapointe at the Université de Montréal and colleagues have used MC and MD simulations to show that indeed these protein pores can be filled with water (a pathway of about 100 molecules) which allows passive water permeation (L. J. Sasseville et al., Biophys. J. 101, 1887-1895; 2011 – paper here). This pathway depends on the proteins’ conformation: there is a constriction at one point which reduces the water bridge to a single-molecule chain which then ‘snaps’ at a ‘hydrophobic plug’, creating a 4.3 Å gap of low water density. But the resulting barrier to water permeation is conformation-dependent, and can be altered by varying the membrane potential. The passage of a sugar molecule also can bring water with it, but the mechanism of this is still open to debate.
Jhih-Wei Chu and colleagues at Berkeley conclude from MD simulations that the insolubility of cellulose in water is an entropic effect due primarily to the reduction of solvent entropy if the glucan chains in a fibril unravel (A. S. Gross et al., J. Phys. Chem. B 115, 13433; 2011 – paper here). There are some lessons here for how to solubilize cellulose in other solvents, such as ionic liquids.
Why and how do ions segregate at the air-water interface? This phenomenon seems well attested, with anions, especially large and polarisable ones, tending to accumulate at the interface. But the reason for this is still debated. Yi Qin Gao if the Beijing National Laboratory for Molecular Sciences and coworkers investigate the question with MD simulations, looking in particular at the differences in how anions and cations are solvated (L. Yang et al., J. Phys. Chem. B jp207652h – paper here). They argue that these differences are due to the charge distribution in the water molecules themselves, and that water can approach anions more closely than cations. They suggest that these differences in hydration account for why anions tend to populate the interface more readily.
And on the same topic, Pavel Jungwirth and colleagues have looked at how the hydration of guanidinium ions affects their orientation at the air-water interface (E. Wernersson et al., J. Phys. Chem. B jp207499s – paper here). Guanidinium is depleted at the interface, but the ions that do stay there are preferentially oriented parallel to the surface: in this configuration, it can sit at the surface without needing to break hydrogen bonds. Another way of looking at this is that the ions can take advantage of the deficit of hydrogen bonds between waters at the surface. The authors suggest that similar reasoning might account for the unexpected orientation of some arginine groups (with an analogous structure) in protein side chains.
I’ve recently written a News & Views article for Nature (478, 467; 2011 – here) about, among other things, the recent paper by George Whitesides’ group (PNAS 108, 17889; 2011 – paper here) on the hydrophobic effect in ligand binding – which, as discussed in the previous post, suggests that there is not any single ‘hydrophobic effect’ operating here, but a delicate and case-specific balance of enthalpic and entropic effects. They noted that in the example they studied, the ‘hydrophobic’ aspect of binding was driven largely by the enthalpic effect of displacing/rearranging water around nonpolar contacts. That notion is supported by a paper by Stephen Martin and colleages at the University of Texas at Austin, who find something rather similar for small peptide binding by the SH2 domain of the growth receptor binding protein Grb2 (J. M. Myslinski et al., JACS 133, 18518; 2011 – paper here). They say that increases in the nonpolar contact area don’t necessarily lead to entropic gains due to release of water, but have a primarily enthalpic influence on binding affinity.
How quickly drugs bind to their target molecules can have important pharmacological implications, but these kinetics are generally poorly understood, and thus to design rationally. Xavier Barril from the University of Barcelona and colleagues show using MD simulations that slow kinetics are often a consequence of the presence of buried polar atoms which form hydrogen bonds that are shielded from water, because of the slowness of dehydration/rehydration (P. Schmidtke et al., JACS ja207494u – paper here). In other words, the pace of events in binding can be set by the degree of water accessibility. They show that this effect can be predicted from structural data, and can thus potentially be accessible to design.
Knowing the hydration structure of proteins is important for small-/wide-angle X-ray scattering (SWAXS) studies of proteins not so much for its own sake but because the contribution of the solvent to the scattering must be subtracted in order to extract information about the protein secondary structure. It’s easy enough to extract the contribution of bulk water, but correcting for the scattering of the hydration shell is complicated. Tobin Sosnick and coworkers at the University of Chicago now show two ways to do this (J. J. Virtanen et al., Biophys. J. 101, 2061-2069; 2011 – paper here). One is to deduce the solvation structure by full MD simulations, which they say gives results that match the SWAXS data closely. But they have also developed a much more computationally less intense solvation model called HyPred, which gives a scattering profile that agrees well both with MD and with experiment.
Bernhardt Trout and his coworkers at MIT present an illustration of just how complex the interactons of proteins and ions can be (D. Shukla et al., JACS ja205215t – paper here). Complex ions such as guanidinium create a particularly intricate picture. Gdm+ can destabilize proteins via the formation of hydrogen bonds and electrostatic interactions, but when paired with an anion that is a hydrogen-bonding acceptor it can form clusters with the ions, which suppresses the effect. Molecules (such as arginine) with multiple Gdm+ groups are sometimes used to suppress protein aggregation, and can do so without compromising protein stability. Trout and colleagues investigate the effect of arginine oligomers (n=1-4) on protein aggregation and conformational stability for two different anions, chloride and sulphate. While monomeric arginine chloride is used as an aggregation suppressor, the n-mers only inhibit aggregation at low concentration – they actually accelerate it at moderate to high concentration. Meanwhile, the sulphates inhibit aggregation at all concentrations. And while the chlorides reduce protein stability, the sulphates enhance it. The researchers explain all this in terms of the balance between ion-ion and ion-protein interactions.
All this mirrors an increasing tendency to consider Hofmeister effects of ions on proteins in terms of direct interactions between the two species, rather than as indirect consequences of changes in hydration. Elena Algaer and Nico van der Vegt at the TU Darmstadt provide some support for this notion with a study of the salting-in and –out of small model amides by various sodium salts (J. Phys. Chem. B jp208583w – paper here). They say, for example, that the salting-in if NiPAM by NaI is mediated by interactions of iodide with the nonpolar groups. Such interactions also explain why, of all the salts studied, the iodide alone fails to induce hydrophobic collapse of polyNiPAM.
How does water permeate cell membranes? Its passage through the water-regulating membrane protein aquaporin is fairly well studied, but little is known about other water transporters. The bacterial sodium-galactose transporter vSGLT and its human homologue the sodium-glucose cotransporter hSGLT1 both have the potential to let water through. Jean-Yves Lapointe at the Université de Montréal and colleagues have used MC and MD simulations to show that indeed these protein pores can be filled with water (a pathway of about 100 molecules) which allows passive water permeation (L. J. Sasseville et al., Biophys. J. 101, 1887-1895; 2011 – paper here). This pathway depends on the proteins’ conformation: there is a constriction at one point which reduces the water bridge to a single-molecule chain which then ‘snaps’ at a ‘hydrophobic plug’, creating a 4.3 Å gap of low water density. But the resulting barrier to water permeation is conformation-dependent, and can be altered by varying the membrane potential. The passage of a sugar molecule also can bring water with it, but the mechanism of this is still open to debate.
Jhih-Wei Chu and colleagues at Berkeley conclude from MD simulations that the insolubility of cellulose in water is an entropic effect due primarily to the reduction of solvent entropy if the glucan chains in a fibril unravel (A. S. Gross et al., J. Phys. Chem. B 115, 13433; 2011 – paper here). There are some lessons here for how to solubilize cellulose in other solvents, such as ionic liquids.
Why and how do ions segregate at the air-water interface? This phenomenon seems well attested, with anions, especially large and polarisable ones, tending to accumulate at the interface. But the reason for this is still debated. Yi Qin Gao if the Beijing National Laboratory for Molecular Sciences and coworkers investigate the question with MD simulations, looking in particular at the differences in how anions and cations are solvated (L. Yang et al., J. Phys. Chem. B jp207652h – paper here). They argue that these differences are due to the charge distribution in the water molecules themselves, and that water can approach anions more closely than cations. They suggest that these differences in hydration account for why anions tend to populate the interface more readily.
And on the same topic, Pavel Jungwirth and colleagues have looked at how the hydration of guanidinium ions affects their orientation at the air-water interface (E. Wernersson et al., J. Phys. Chem. B jp207499s – paper here). Guanidinium is depleted at the interface, but the ions that do stay there are preferentially oriented parallel to the surface: in this configuration, it can sit at the surface without needing to break hydrogen bonds. Another way of looking at this is that the ions can take advantage of the deficit of hydrogen bonds between waters at the surface. The authors suggest that similar reasoning might account for the unexpected orientation of some arginine groups (with an analogous structure) in protein side chains.
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